Mercurial > repos > iuc > moabs
changeset 1:8c8cc81b34cd draft
"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761"
| author | iuc |
|---|---|
| date | Sat, 11 Apr 2020 04:14:34 -0400 |
| parents | 26d7ec4af119 |
| children | 214874e24cd6 |
| files | macros.xml moabs.xml test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr |
| diffstat | 8 files changed, 642 insertions(+), 60 deletions(-) [+] |
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--- a/macros.xml Fri Sep 06 09:54:27 2019 -0400 +++ b/macros.xml Sat Apr 11 04:14:34 2020 -0400 @@ -8,16 +8,32 @@ <token name="@VERSION@">1.3.4.6</token> + <token name="@DMCExample@"> + +Example:: + + chr11 87 89 6 1 0.652,1 10 0.2 0,0.47 -0.8 -0.327 -0.857,-0.327 0.000318 0.00699 strongHypo + chr11 152 154 4 1 0.549,1 9 0.333 0.0575,0.609 -0.667 -0.113 -0.761,-0.113 0.0035 0.0699 hypo + chr11 258 260 3 1 0.473,1 13 0.231 0,0.466 -0.769 -0.165 -0.809,-0.165 0.00236 0.0357 hypo + chr11 331 333 6 0.667 0.341,0.992 22 0.227 0.0499,0.405 -0.439 -0.058 -0.66,-0.058 0.00636 0.0638 hypo + chr11 630 632 3 1 0.473,1 5 0 0,0.393 -1 -0.271 -1,-0.271 0.000954 0.0179 strongHypo + chr11 638 640 3 0.667 0.249,1 5 0.6 0.264,0.936 -0.0667 -0 -0.461,0.418 0.0286 1 hypo + chr11 641 643 4 1 0.549,1 5 0.4 0.064,0.736 -0.6 -0.0122 -0.748,-0.0122 0.00715 0.167 hypo + chr11 645 647 4 1 0.549,1 8 1 0.717,1 0 0 -0.183,0.374 0.067 1 hypo + chr11 666 668 4 1 0.549,1 9 0.667 0.391,0.942 -0.333 -0 -0.506,0.15 0.021 0.497 hypo + chr11 685 687 3 1 0.473,1 8 0 0,0.283 -1 -0.342 -1,-0.342 0.000364 0.00606 strongHypo + + </token> + <token name="@DMRExample@"> Example:: - chr11 316 1705 - 35 30 5 -1 - chr11 3052 3674 - 17 16 1 -1 - chr11 18599 19013 - 9 7 3 -1 - chr11 19120 19931 - 39 39 0 -1 - chr11 22138 22618 - 14 12 3 -1 - chr11 28140 28356 - 4 4 0 -1 + chr11 2529 2582 0.787 77 8 0.226 123 8 -0.204 3.79e-17 strongHypo + chr11 2976 3065 0.833 222 3 0.241 116 3 -0.339 1.69e-22 strongHypo + chr11 4327 5335 0.722 286 29 0.143 563 29 -0.201 2.3e-48 strongHypo + chr11 6544 7008 0.955 86 17 0.126 97 17 -0.223 6.5e-34 strongHypo + </token> <xml name="citations">
--- a/moabs.xml Fri Sep 06 09:54:27 2019 -0400 +++ b/moabs.xml Sat Apr 11 04:14:34 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@"> +<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@+galaxy1"> <description>MOdel based Analysis of Bisulfite Sequencing data</description> <macros> <import>macros.xml</import> @@ -11,10 +11,13 @@ #end if moabs -v 1 --def MMAP.p="\${GALAXY_SLOTS:-4}" --def MCALL.p="\${GALAXY_SLOTS:-4}" --def MCOMP.p="\${GALAXY_SLOTS:-4}" --cf '$cfg_file' && #if "1" in $output_selector: - cp -f dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr '$output1' && + cp -f dmc_M2_g1.G.bed_vs_g2.G.bed.txt '$output1' && #end if #if "2" in $output_selector: - cp -f comp.g1.vs.g2.txt '$output2' && + cp -f dmr_M2_g1.G.bed_vs_g2.G.bed.txt '$output2' && + #end if + #if "3" in $output_selector: + cp -f comp.g1.vs.g2.txt '$output3' && #end if echo Done ]]> @@ -62,18 +65,54 @@ #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0": v=$bsmap_advanced.bsmap_mismatch.v #end if + s=$bsmap_advanced.s + w=$bsmap_advanced.w + #if $bsmap_advanced.D: + D=$bsmap_advanced.D + #end if + S=$bsmap_advanced.S n=$bsmap_advanced.n + q=$bsmap_advanced.q + z=$bsmap_advanced.z + f=$bsmap_advanced.f + #if $bsmap_advanced.A: + A=$bsmap_advanced.A + #end if r=$bsmap_advanced.r - R='' + #if str( $bsmap_advanced.R ) == "1": + R='' + #end if + #if str( $bsmap_advanced.u ) == "1": + u='' + #end if + m=$bsmap_advanced.m + x=$bsmap_advanced.x [MCALL] Path=mcall r='${reference_fasta_filename}' + cytosineMinScore=$mcall_advanced.cytosineMinScore + nextBaseMinScore=$mcall_advanced.nextBaseMinScore + qualityScoreBase=$mcall_advanced.qualityScoreBase + trimWGBSEndRepairPE2Seq=$mcall_advanced.trimWGBSEndRepairPE2Seq + trimWGBSEndRepairPE1Seq=$mcall_advanced.trimWGBSEndRepairPE1Seq + processPEOverlapSeq=$mcall_advanced.processPEOverlapSeq + trimRRBSEndRepairSeq=$mcall_advanced.trimRRBSEndRepairSeq + minFragSize=$mcall_advanced.minFragSize + minMMFragSize=$mcall_advanced.minMMFragSize + reportCpX=$mcall_advanced.reportCpX [MCOMP] Path=mcomp - reference='${reference_fasta_filename}' doComp=$mcomp_advanced.doComp.compare_selector + d=$mcomp_advanced.d + filterCredibleDif=$mcomp_advanced.filterCredibleDif + pFetDmc=$mcomp_advanced.pFetDmc + pFetDmr=$mcomp_advanced.pFetDmr + minNominalDif=$mcomp_advanced.minNominalDif + minCredibleDif=$mcomp_advanced.minCredibleDif + minDmcsInDmr=$mcomp_advanced.minDmcsInDmr + maxDistConsDmcs=$mcomp_advanced.maxDistConsDmcs </configfile> </configfiles> @@ -134,9 +173,10 @@ </conditional> </repeat> <section name="bsmap_advanced" title="Advanced options for BSMAP" expanded="False"> + <param argument="-s" type="integer" value="16" min="8" max="16" label="Seed size" help="The seed size for the HASH table. BSMAP implements a seeding algorithm by indexing reference for all possible k-mers, i.e. seeds. As for the seed size, i.e. the length of k-mers, 16 is suggested for the WGBS mode, and 12 is suggested for the RRBS mode. Min=8, max=16."/> <conditional name="bsmap_mismatch"> - <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help=""> - <option value="0">Do not set</option> + <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="When `Do not set` selected, BSMAP will allow a default suggested 8% mismatch rate. Otherwise, a customized mismatch can be controlled by specifying a mismatch rate or a mismatch number."> + <option value="0" selected="true">Do not set</option> <option value="1">Set the mismatch rate</option> <option value="2">Set the mismatch number</option> </param> @@ -147,44 +187,102 @@ <param argument="-v" type="integer" value="3" min="0" label="Mismatch number" help="The maximum number of mismatches allowed on a read"/> </when> </conditional> - <param argument="-n" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Mapping to four strands?" help="Yes: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --; No: only map to 2 forward strands, i.e. BSW(++) and BSC(-+)"/> - <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow)"> + <param argument="-w" type="integer" value="1000" min="0" max="1000" label="Maximum number of equal best hits to count" help="Maximum number of equal best hits to count. When multiple mapping occurs for a read, it should control the number of records to report. Default: 1000."/> + <param argument="-D" type="text" label="Restriction enzyme digestion sites for RRBS mode" help="For RRBS data, this option activates RRBS mapping mode and set restriction enzyme digestion sites. Digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (WGBS mode)."> + <validator type="regex" message="Use A/T/C/G/- for restriction enzyme digestion sites">^[ATCG-]*$</validator> + </param> + <param argument="-S" type="integer" value="0" label="Random seed" help="Seed for random number generation used in selecting multiple hits. Other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. Default=0 (get seed from system clock, mapping results not resproducible)."/> + <param argument="-n" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Mapping to four strands?" help="Yes: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, --; No: only map to 2 forward strands, i.e. BSW(++) and BSC(-+). For example, for a traditional library construction, two forward strands, ++ and -+, are sufficient for alignments. However, a Pico library construction needs all four-strand mappings."/> + <param argument="-q" type="integer" value="0" min="0" max="40" label="Quality threshold in trimming" help="The quality threshold to trim read bases. To obtain an accurate mapping, low-quality bases should be skipped beforehand. Min=0, max=40. Default=0 (no trim)."/> + <param argument="-z" type="select" label="Base quality" help="Base quality for sequencing reads, Illumina or Sanger."> + <option value="33" selected="true">Sanger</option> + <option value="64">Illumina</option> + </param> + <param argument="-f" type="integer" value="5" min="0" label="Maximum number of Ns in a read to filter out" help="To filter out low-quality reads containing >n Ns. Default=5."/> + <param argument="-A" type="text" label="3' adapter sequence to trim" help="To trim 3' adapter sequence. Default: none (no trim)."> + <validator type="regex" message="Use A/T/C/G for adapter sequences, and the length should be greater equal to 12 bases.">^[ATCG]{12,}$|^$</validator> + </param> + <param argument="-r" type="select" label="How to report repeat hits" help="0=none(unique hit/pair); 1=random one; 2=all(slow). When input reads coverage is high, it is suggested to report only unique hits (r=0). For a low-depth library, a random one from multiple mappings (r=1), or all multiple mappings (r=2) can be specified to increase read coverage, yet be cautious about bias caused by ambiguous mappings."> <option value="0" selected="true">0</option> <option value="1">1</option> <option value="2">2</option> </param> + <param argument="-R" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Print corresponding reference sequences?" help="Yes: print corresponding reference sequences in mapping records, a `RS:` tag will be added in record attributes; No: do not print reference sequences."/> + <param argument="-u" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Report unmapped reads?" help="Yes: print unmapped reads; No: do not print unmapped reads."/> + <param argument="-m" type="integer" value="28" min="0" label="Minimal insert size allowed in paired-end mapping" help="For paired-end reads, the minimal insert size allowed in two end mapping. Default=28."/> + <param argument="-x" type="integer" value="1000" min="0" label="Maximal insert size allowed in paired-end mapping" help="For paired-end reads, the maximal insert size allowed in two end mapping. Default=1000."/> + </section> + <section name="mcall_advanced" title="Advanced options for MCALL" expanded="False"> + <param argument="--cytosineMinScore" type="integer" value="20" min="0" label="Threshold for cytosine quality score" help="Threshold for cytosine quality score. Discard the base if threshold is not reached. Default=20."/> + <param argument="--nextBaseMinScore" type="integer" value="3" min="-1" label="Threshold for the next base quality score" help="Threshold for the next base quality score. Possible values: -1 makes the program not to check if next base matches reference; any positive integer or zero makes the program to check if next base matches reference and reaches this score threshold; default=3, i.e., better than 'B' or '#'."/> + <param argument="--qualityScoreBase" type="select" label="Specify the quality score system" help="Sanger, Solexa, or Illumina. See wiki FASTQ_format for details. Default: auto-detection."> + <option value="0" selected="true">Auto-detection</option> + <option value="33">Sanger</option> + <option value="59">Solexa</option> + <option value="64">Illumina</option> + </param> + <param argument="--trimWGBSEndRepairPE2Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from +-/--" help="To trim end-repair sequence from begin of +-/-- reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from begin of +-/-- reads. Default: trim 3 bases."/> + <param argument="--trimWGBSEndRepairPE1Seq" type="integer" value="3" min="0" label="Bases to trim end-repair sequences from ++/-+" help="To trim end-repair sequence from end of ++/-+ reads from Pair End WGBS Sequencing. 0: no trim; n (positive integer): trim n bases from end of ++/-+ reads. Default: trim 3 bases."/> + <param argument="--processPEOverlapSeq" type="select" label="Count once or twice the overlap sequence of two pairs" help="Two ends of paired-end reads may be overlapped in mapping. The overlap sequencce will be counted once or twice for cytosine methylation measurements. Default: once."> + <option value="1" selected="true">Once</option> + <option value="0">Twice</option> + </param> + <param argument="--trimRRBSEndRepairSeq" type="select" label="How to trim end-repair sequence for RRBS reads?" help="To trim end-repair sequence for RRBS reads. 0: no trim; 2: trim the last CG at exactly end of ++/-+ reads and trim the first CG at exactly begin of +-/-- reads like the WGBS situation. Default=2."> + <option value="2" selected="true">2</option> + <option value="0">0</option> + </param> + <param argument="--minFragSize" type="integer" value="0" min="0" label="Minimal fragment size for properly mapped reads" help="To retain properly mapped and large enough fragment sizes. The 9th field in the BAM file is the fragment size of the mapping, and non-properly-paired read has 0 at the 9th field. This option is set to require properly paired and large enough fragment size. Default=0 for all records."/> + <param argument="--minMMFragSize" type="integer" value="0" min="0" label="Minimal fragment size for multiply matched read" help="Same as --minFragSize but this option is only applicable to reads with flag 0x100 set as 1, i.e., reads multiply mapped. Default=0 for all records."/> + <param argument="--reportCpX" type="select" label="Generates CpG/A/C/T methylation?" help="To generate methylation for CpG, or CpA/CpC/CpT. Default=CpG."> + <option value="G" selected="true">CpG</option> + <option value="C">CpC</option> + <option value="A">CpA</option> + <option value="T">CpT</option> + </param> </section> <section name="mcomp_advanced" title="Advanced options for MCOMP" expanded="False"> <conditional name="doComp"> <param name="compare_selector" type="select" label="Run the comparison or not" help="Yes: compare; No: do not compare, using the comparison result by `-c`"> - <option value="1">Yes</option> + <option value="1" selected="true">Yes</option> <option value="0">No</option> </param> <when value="0"> <param argument="-c" name="compFile" type="data" format="txt" label="Input comparison results" help="Previously generated comparison file from history"/> </when> </conditional> + <param argument="-d" type="integer" value="3" min="0" label="Minimum depth for a site coverage" help="If a site has depth less than `d`, this site is ignored for statistical tests. This option affects much of nominal ratios but none of credible ratios. This option may be reset during later DMC/DMR rescan to filter sites with depth less than `d`. Default=3."/> + <param argument="--filterCredibleDif" type="float" value="-10" label="Minimum absolute credible methylation difference (CDIF)" help="If absolute value of CDIF for a site less than filterCredibleDif, this site is ignored for regional calculation. Use a small value, such as 0.01, to filter all sites with no difference; use 0.20 (for example) to select DMCs. Any negative number means no filter. Default=-10."/> + <param argument="--pFetDmc" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMC scan" help="Cutoff of P value from Fisher Exact Test for DMC scan. Default=`0.05`."/> + <param argument="--pFetDmr" type="float" value="0.05" min="0" max="1" label="Cutoff of Pvalue from Fisher Exact Test for DMR scan" help="Cutoff of P value from Fisher Exact Test for DMR scan. Default=`0.05`."/> + <param argument="--minNominalDif" type="float" value="0.33333" min="0" max="1" label="Minimal nominal methylation difference for DMC and DMR calling" help="Minimal nominal methylation difference for DMC and DMR. Default=`0.3333`."/> + <param argument="--minCredibleDif" type="float" value="0.2" min="0" max="1" label="Minimal credible methylation difference for DMC calling" help="Minimal CDIF for DMC calling. Default=`0.2`."/> + <param argument="--minDmcsInDmr" type="integer" value="3" min="1" label="Minimum number of DMCs in a DMR" help="Minimum number of DMCs in a DMR. Default=3."/> + <param argument="--maxDistConsDmcs" type="integer" value="300" min="1" label="Maximum distance between two consective DMCs for a DMR" help="Maximum distance between two consective DMCs for a DMR. Default=300."/> </section> <param name="output_selector" type="select" multiple="true" optional="true" label="Select output files" help=""> - <option value="1"> dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr </option> - <option value="2"> comp.g1.vs.g2.txt </option> - <option value="3"> BAM files </option> - <option value="4"> Methylation calling BED files </option> + <option value="1" selected="true">dmc_M2_g1.G.bed_vs_g2.G.bed.txt</option> + <option value="2" selected="true">dmr_M2_g1.G.bed_vs_g2.G.bed.txt</option> + <option value="3" selected="true">comp.g1.vs.g2.txt</option> + <option value="4" selected="true">BAM files</option> + <option value="5" selected="true">Methylation calling BED files</option> </param> </inputs> <outputs> - <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr"> + <data name="output1" format="interval" label="${tool.name} on ${on_string} : dmc_M2_g1.G.bed_vs_g2.G.bed.txt"> <filter> "1" in output_selector </filter> </data> - <data name="output2" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt"> + <data name="output2" format="interval" label="${tool.name} on ${on_string} : dmr_M2_g1.G.bed_vs_g2.G.bed.txt"> <filter> "2" in output_selector </filter> </data> + <data name="output3" format="interval" label="${tool.name} on ${on_string} : comp.g1.vs.g2.txt"> + <filter> "3" in output_selector </filter> + </data> <collection name="output_collection_bam" type="list" label="BAM files"> - <filter> "3" in output_selector </filter> + <filter> "4" in output_selector </filter> <discover_datasets pattern="(?P<designation>.+\.bam$)" ext='bam'/> </collection> <collection name="output_collection_bed" type="list" label="Methylation calling BED files"> - <filter> "4" in output_selector </filter> + <filter> "5" in output_selector </filter> <discover_datasets pattern="(?P<designation>g[12]\.G\.bed$)" ext='interval'/> </collection> </outputs> @@ -226,14 +324,15 @@ <param name="compare_selector" value="1"/> </conditional> --> - <param name="output_selector" value="1,2,3,4"/> - <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/> - <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> + <param name="output_selector" value="1,2,3,4,5"/> + <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> <output_collection name="output_collection_bam" count="4"> - <element name="g1_r1.bam" file="SE_g1_r1.bam" compare="sim_size"/> - <element name="g1_r2.bam" file="SE_g1_r2.bam" compare="sim_size"/> - <element name="g2_r1.bam" file="SE_g2_r1.bam" compare="sim_size"/> - <element name="g2_r2.bam" file="SE_g2_r2.bam" compare="sim_size"/> + <element name="g1_r1.bam" file="SE_g1_r1.bam" ftype="bam" lines_diff="2"/> + <element name="g1_r2.bam" file="SE_g1_r2.bam" ftype="bam" lines_diff="2"/> + <element name="g2_r1.bam" file="SE_g2_r1.bam" ftype="bam" lines_diff="2"/> + <element name="g2_r2.bam" file="SE_g2_r2.bam" ftype="bam" lines_diff="2"/> </output_collection> <output_collection name="output_collection_bed" count="2"> <element name="g1.G.bed" file="SE_g1.G.bed" ftype="interval" lines_diff="1"/> @@ -267,9 +366,10 @@ <param name="compare_selector" value="1"/> </conditional> --> - <param name="output_selector" value="1,2"/> - <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/> - <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> + <param name="output_selector" value="1,2,3"/> + <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> </test> <test> <!-- test paired collection --> @@ -306,9 +406,10 @@ <param name="compare_selector" value="1"/> </conditional> --> - <param name="output_selector" value="1,2"/> - <output name="output1" file="PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/> - <output name="output2" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> + <param name="output_selector" value="1,2,3"/> + <output name="output1" file="PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output2" file="PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output3" file="PE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> </test> <test> <!-- test data table reference --> @@ -347,9 +448,10 @@ <param name="compare_selector" value="1"/> </conditional> --> - <param name="output_selector" value="1,2"/> - <output name="output1" file="SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr" ftype="interval" lines_diff="1"/> - <output name="output2" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> + <param name="output_selector" value="1,2,3"/> + <output name="output1" file="SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output2" file="SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt" ftype="interval" lines_diff="1"/> + <output name="output3" file="SE_comp.g1.vs.g2.txt" ftype="interval" lines_diff="1"/> </test> </tests> <help> @@ -376,31 +478,63 @@ **Outputs** -Four output files can be selected to report, namely +Five output files can be selected to report, namely - 1. **DMR region file** - the major result file - 2. **Comparison file between two groups** - the intermediate comparion result - 3. **BAM files** - intermediate BAM files - 4. **Methylation BED files** - intermediate methylation BED files + 1. **DMC site file** - the major DMC result file + 2. **DMR region file** - the major DMR result file + 3. **Comparison file between two groups** - the intermediate comparion result + 4. **BAM files** - intermediate BAM files + 5. **Methylation BED files** - intermediate methylation BED files ----- -MOABS will detect differential methylated regions (DMRs) using the input BS-Seq -reads. The output file is a tab-delimited text file (not strictly a BED -format), representing DMRs. It has 8 columns as below. +MOABS detects differentially methylated cytosines (DMCs) and differentially +methylated regions (DMRs) using the input BS-Seq reads. The output DMC and DMR +file are tab-delimited text files (not strictly a BED format), representing +DMCs and DMRs. + +A DMC site file has 15 columns as below. + +chrom<TAB>start<TAB>end<TAB>totalC_0<TAB>nominalRatio_0<TAB>ratioCI_0<TAB>totalC_1<TAB>nominalRatio_1<TAB>ratioCI_1<TAB>nominalDif_1-0<TAB>credibleDif_1-0<TAB>difCI_1-0<TAB>p_sim_1_v_0<TAB>p_fet_1_v_0<TAB>class -chrom<TAB>start<TAB>end<TAB>methylation_state<TAB>CpGsites<TAB>DMCcount<TAB>nonDMCcount<TAB>hidden_state + 1. **chrom** - The chromosome of the CpG site. + 2. **start** - The start genomic locus of the CpG site. + 3. **end** - The end genomic locus of the CpG site. + 4. **totalC_0** - The total number of CpG read coverage in group 0. + 5. **nominalRatio_0** - The nominal methylation ratio of the CpG in group 0. + 6. **ratioCI_0** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 0. + 7. **totalC_1** - The total number of CpG read coverage in group 1. + 8. **nominalRatio_1** - The nominal methylation ratio of the CpG in group 1. + 9. **ratioCI_1** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 1. + 10. **nominalDif_1-0** - The nominal methylation difference between the group 1 and the group 0. + 11. **credibleDif_1-0** - The credible methylation difference (CDIF) between the group 1 and the group 0. + 12. **difCI_1-0** - The difference of ratio CIs between the group 1 and the group 0. + 13. **p_sim_1_v_0** - P-value according to the similarity probablities. + 14. **p_fet_1_v_0** - P-value according to the Fisher exact test. + 15. **class** - 5-state class labels by methylation differences and p-values. + +For example, CpGs in the DMC file are recorded in the following format. + +@DMCExample@ + +A DMR result file has 12 columns as below. + +chrom<TAB>start<TAB>end<TAB>meanRatio_0<TAB>totalC_0<TAB>cSites_0<TAB>meanRatio_1<TAB>totalC_1<TAB>cSites_1<TAB>methDif_1-0<TAB>p_1_v_0<TAB>class_1_v_0 1. **chrom** - The chromosome of the region. 2. **start** - The start genomic locus of the region. 3. **end** - The end genomic locus of the region. - 4. **methylation_state** - The methylation state of the region, "+"/"-" representing hyper- or hypo-methylation regions. - 5. **CpGsites** - Total number of CpG sites in the region. - 6. **DMCcount** - The number of differential methylated CpG sites (DMCs) in the region. - 7. **nonDMCcount** - The number of non-DMCs in the region. - 8. **hidden_state** - The hidden state prediced by Hidden Markov Model (HMM), "1"/"-1" representing hyper- or hypo-methylation states. + 4. **meanRatio_0** - Mean methylation ratio of the region in group 0. + 5. **totalC_0** - Total cytosine coverage of the region in group 0. + 6. **cSites_0** - The number of CpG sites of the region in group 0. + 7. **meanRatio_1** - Mean methylation ratio of the region in group 1. + 8. **totalC_1** - Total cytosine coverage of the region in group 1. + 9. **cSites_1** - The number of CpG sites of the region in group 1. + 10. **methDif_1-0** - Average methylation difference of the region between group 1 and group 0. + 11. **p_1_v_0** - P-value from Fisher exact test of the region between group 1 and group 0. + 12. **class_1_v_0** - 5-state class labels for the DMR. -For example, six DMRs are identified in the following format. +For example, four DMRs are identified in the following format. @DMRExample@
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 @@ -0,0 +1,122 @@ +#chrom start end totalC_0 nominalRatio_0 ratioCI_0 totalC_1 nominalRatio_1 ratioCI_1 nominalDif_1-0 credibleDif_1-0 difCI_1-0 p_sim_1_v_0 p_fet_1_v_0 class +seg 87 89 6 1 0.652,1 10 0.2 0,0.47 -0.8 -0.327 -0.857,-0.327 0.000318 0.00699 strongHypo +seg 152 154 4 1 0.549,1 9 0.333 0.0575,0.609 -0.667 -0.113 -0.761,-0.113 0.0035 0.0699 hypo +seg 258 260 3 1 0.473,1 13 0.231 0,0.466 -0.769 -0.165 -0.809,-0.165 0.00236 0.0357 hypo +seg 331 333 6 0.667 0.341,0.992 22 0.227 0.0499,0.405 -0.439 -0.058 -0.66,-0.058 0.00636 0.0638 hypo +seg 630 632 3 1 0.473,1 5 0 0,0.393 -1 -0.271 -1,-0.271 0.000954 0.0179 strongHypo +seg 638 640 3 0.667 0.249,1 5 0.6 0.264,0.936 -0.0667 -0 -0.461,0.418 0.0286 1 hypo +seg 641 643 4 1 0.549,1 5 0.4 0.064,0.736 -0.6 -0.0122 -0.748,-0.0122 0.00715 0.167 hypo +seg 645 647 4 1 0.549,1 8 1 0.717,1 0 0 -0.183,0.374 0.067 1 hypo +seg 666 668 4 1 0.549,1 9 0.667 0.391,0.942 -0.333 -0 -0.506,0.15 0.021 0.497 hypo +seg 685 687 3 1 0.473,1 8 0 0,0.283 -1 -0.342 -1,-0.342 0.000364 0.00606 strongHypo +seg 689 691 4 1 0.549,1 9 0.667 0.391,0.942 -0.333 -0 -0.506,0.15 0.021 0.497 hypo +seg 697 699 3 1 0.473,1 7 0.571 0.27,0.872 -0.429 -0 -0.595,0.156 0.017 0.475 hypo +seg 699 701 3 1 0.473,1 9 1 0.741,1 0 0 -0.149,0.454 0.0596 1 hypo +seg 820 822 7 0.857 0.529,1 20 0.4 0.2,0.6 -0.457 -0.0729 -0.62,-0.0729 0.00528 0.0768 hypo +seg 830 832 7 0.857 0.529,1 18 0.222 0.0252,0.419 -0.635 -0.236 -0.766,-0.236 0.000768 0.0068 strongHypo +seg 842 844 4 0.75 0.343,1 10 0.3 0.035,0.565 -0.45 -0 -0.672,0.0536 0.0117 0.245 hypo +seg 1172 1174 3 1 0.473,1 12 0.333 0.0889,0.578 -0.667 -0.0658 -0.738,-0.0658 0.005 0.0769 hypo +seg 1180 1182 3 1 0.473,1 11 0.0909 0,0.339 -0.909 -0.286 -0.909,-0.286 0.000705 0.011 strongHypo +seg 1201 1203 3 0.667 0.249,1 14 0.214 0,0.44 -0.452 -0 -0.7,0.0401 0.0118 0.191 hypo +seg 1203 1205 3 0.667 0.249,1 13 0.308 0.0724,0.543 -0.359 -0 -0.629,0.133 0.0176 0.518 hypo +seg 1303 1305 3 1 0.473,1 4 0 0,0.451 -1 -0.229 -1,-0.229 0.00143 0.0286 strongHypo +seg 1333 1335 4 0.25 0,0.657 6 0.167 0,0.521 -0.0833 -0 -0.47,0.291 0.0339 1 hypo +seg 1343 1345 3 0 0,0.527 10 0.2 0,0.47 0.2 0 -0.318,0.357 0.0363 1 hypo +seg 2310 2312 8 1 0.717,1 11 0.455 0.198,0.711 -0.545 -0.162 -0.69,-0.162 0.00184 0.0181 hypo +seg 2336 2338 8 1 0.717,1 5 0.6 0.264,0.936 -0.4 -0.0115 -0.656,-0.0115 0.0099 0.128 hypo +seg 2396 2398 8 1 0.717,1 12 0.333 0.0889,0.578 -0.667 -0.273 -0.774,-0.273 0.000439 0.0047 strongHypo +seg 2488 2490 3 0.333 0,0.751 7 0 0,0.312 -0.333 -0 -0.669,0.0603 0.0175 0.3 hypo +seg 2516 2518 7 0.571 0.27,0.872 16 0.5 0.278,0.722 -0.0714 -0 -0.372,0.269 0.0377 1 hypo +seg 2529 2531 7 0.571 0.27,0.872 25 0.04 0,0.17 -0.531 -0.203 -0.745,-0.203 0.000552 0.00445 strongHypo +seg 2548 2550 10 0.7 0.435,0.965 17 0.0588 0,0.238 -0.641 -0.303 -0.787,-0.303 0.000131 0.000939 strongHypo +seg 2550 2552 10 0.8 0.53,1 20 0.4 0.2,0.6 -0.4 -0.0665 -0.586,-0.0665 0.00582 0.0577 hypo +seg 2556 2558 11 0.636 0.382,0.891 19 0.0526 0,0.216 -0.584 -0.271 -0.746,-0.271 0.000167 0.0011 strongHypo +seg 2567 2569 9 0.889 0.606,1 11 0.364 0.109,0.618 -0.525 -0.135 -0.697,-0.135 0.0027 0.0281 hypo +seg 2573 2575 10 0.9 0.636,1 12 0.167 0,0.41 -0.733 -0.352 -0.835,-0.352 0.000117 0.00191 strongHypo +seg 2578 2580 9 0.889 0.606,1 10 0.5 0.234,0.766 -0.389 -0.0151 -0.6,-0.0151 0.0092 0.141 hypo +seg 2580 2582 11 0.909 0.661,1 9 0.222 0,0.507 -0.687 -0.287 -0.812,-0.287 0.00036 0.00452 strongHypo +seg 2603 2605 8 1 0.717,1 3 0.333 0,0.751 -0.667 -0.119 -0.834,-0.119 0.00328 0.0545 hypo +seg 2625 2627 8 1 0.717,1 5 0.6 0.264,0.936 -0.4 -0.0115 -0.656,-0.0115 0.0099 0.128 hypo +seg 2641 2643 10 0.9 0.636,1 10 0.2 0,0.47 -0.7 -0.299 -0.817,-0.299 0.00031 0.00548 strongHypo +seg 2645 2647 9 0.667 0.391,0.942 8 0.25 0,0.55 -0.417 -0 -0.642,0.00262 0.00968 0.153 hypo +seg 2659 2661 11 0.727 0.473,0.982 7 0.429 0.128,0.73 -0.299 -0 -0.567,0.0906 0.0183 0.332 hypo +seg 2684 2686 9 0.778 0.493,1 10 0.5 0.234,0.766 -0.278 -0 -0.529,0.0939 0.0198 0.35 hypo +seg 2976 2978 92 0.88 0.811,0.95 49 0.347 0.217,0.477 -0.533 -0.393 -0.639,-0.393 7.62e-11 2.14e-10 strongHypo +seg 2986 2988 122 0.869 0.807,0.93 61 0.377 0.258,0.496 -0.492 -0.368 -0.592,-0.368 1.41e-11 1.77e-11 strongHypo +seg 3063 3065 8 0.75 0.45,1 6 0 0,0.348 -0.75 -0.257 -0.833,-0.257 0.000785 0.00966 strongHypo +seg 3207 3209 3 1 0.473,1 6 0.833 0.479,1 -0.167 -0 -0.397,0.333 0.0373 1 hypo +seg 3405 3407 4 0.75 0.343,1 8 0.25 0,0.55 -0.5 -0 -0.711,0.0288 0.00979 0.222 hypo +seg 3411 3413 4 0.75 0.343,1 9 0.111 0,0.394 -0.639 -0.112 -0.799,-0.112 0.0036 0.0517 hypo +seg 3427 3429 4 1 0.549,1 3 0.667 0.249,1 -0.333 -0 -0.639,0.17 0.0214 0.429 hypo +seg 3429 3431 5 0.8 0.418,1 4 0.5 0.147,0.853 -0.3 -0 -0.611,0.205 0.0214 0.524 hypo +seg 3433 3435 5 1 0.607,1 3 0.333 0,0.751 -0.667 -0.0486 -0.815,-0.0486 0.00572 0.107 hypo +seg 3667 3669 3 1 0.473,1 8 0.125 0,0.429 -0.875 -0.221 -0.88,-0.221 0.00146 0.0242 strongHypo +seg 4037 4039 3 1 0.473,1 8 0.625 0.337,0.913 -0.375 -0 -0.539,0.191 0.0204 0.491 hypo +seg 4046 4048 3 1 0.473,1 7 0.143 0,0.471 -0.857 -0.189 -0.87,-0.189 0.00194 0.0333 hypo +seg 4057 4059 4 1 0.549,1 7 0.429 0.128,0.73 -0.571 -0.0173 -0.71,-0.0173 0.00708 0.194 hypo +seg 4060 4062 4 1 0.549,1 6 0.333 0.0079,0.659 -0.667 -0.0776 -0.778,-0.0776 0.00455 0.0762 hypo +seg 4277 4279 5 0.8 0.418,1 3 0 0,0.527 -0.8 -0.0985 -0.843,-0.0985 0.00381 0.143 hypo +seg 4280 4282 5 0.6 0.264,0.936 3 0.333 0,0.751 -0.267 -0 -0.594,0.282 0.0229 1 hypo +seg 4283 4285 5 0.6 0.264,0.936 4 0 0,0.451 -0.6 -0.0122 -0.748,-0.0122 0.00715 0.167 hypo +seg 4320 4322 4 0.75 0.343,1 4 0 0,0.451 -0.75 -0.0938 -0.834,-0.0938 0.00397 0.143 hypo +seg 4327 4329 4 1 0.549,1 3 0 0,0.527 -1 -0.229 -1,-0.229 0.00143 0.0286 strongHypo +seg 4333 4335 4 1 0.549,1 3 0 0,0.527 -1 -0.229 -1,-0.229 0.00143 0.0286 strongHypo +seg 4340 4342 3 1 0.473,1 3 0 0,0.527 -1 -0.17 -1,-0.17 0.00229 0.1 hypo +seg 4505 4507 5 0.4 0.064,0.736 16 0 0,0.162 -0.4 -0.0844 -0.683,-0.0844 0.00444 0.0476 hypo +seg 4511 4513 6 0.667 0.341,0.992 18 0.167 0,0.359 -0.5 -0.107 -0.709,-0.107 0.00377 0.0381 hypo +seg 4516 4518 6 0.5 0.184,0.816 21 0.0476 0,0.198 -0.452 -0.122 -0.702,-0.122 0.00264 0.0248 hypo +seg 4550 4552 9 0.667 0.391,0.942 23 0.13 0,0.292 -0.536 -0.205 -0.719,-0.205 0.000775 0.00564 strongHypo +seg 4605 4607 8 0.75 0.45,1 26 0 0,0.105 -0.75 -0.408 -0.874,-0.408 2.94e-06 2.08e-05 strongHypo +seg 4648 4650 15 0.667 0.445,0.889 39 0.179 0.0544,0.305 -0.487 -0.232 -0.653,-0.232 0.00023 0.00108 strongHypo +seg 4738 4740 26 0.577 0.398,0.756 53 0.151 0.0496,0.252 -0.426 -0.232 -0.576,-0.232 5.23e-05 0.000172 strongHypo +seg 4797 4799 15 0.6 0.374,0.826 45 0.0889 0,0.188 -0.511 -0.271 -0.68,-0.271 3.55e-05 0.000153 strongHypo +seg 4829 4831 12 0.75 0.505,0.995 38 0.105 0,0.22 -0.645 -0.364 -0.782,-0.364 9.24e-06 4.74e-05 strongHypo +seg 4846 4848 14 0.929 0.721,1 38 0.105 0,0.22 -0.823 -0.574 -0.884,-0.574 1.06e-08 4.75e-08 strongHypo +seg 4922 4924 13 0.538 0.298,0.779 33 0.273 0.123,0.422 -0.266 -0.00424 -0.484,-0.00424 0.0135 0.167 hypo +seg 4925 4927 13 0.615 0.377,0.854 33 0.303 0.15,0.456 -0.312 -0.0403 -0.517,-0.0403 0.00858 0.0916 hypo +seg 4932 4934 15 0.8 0.583,1 29 0.276 0.116,0.435 -0.524 -0.251 -0.671,-0.251 0.000238 0.00138 strongHypo +seg 4949 4951 16 0.625 0.407,0.843 23 0.13 0,0.292 -0.495 -0.224 -0.661,-0.224 0.000359 0.00203 strongHypo +seg 4982 4984 15 0.6 0.374,0.826 11 0.455 0.198,0.711 -0.145 -0 -0.414,0.169 0.034 0.692 hypo +seg 4984 4986 14 0.571 0.338,0.804 11 0.455 0.198,0.711 -0.117 -0 -0.393,0.198 0.0369 0.695 hypo +seg 5011 5013 16 0.375 0.157,0.593 12 0.25 0.00535,0.495 -0.125 -0 -0.364,0.168 0.0389 0.687 hypo +seg 5013 5015 16 0.375 0.157,0.593 11 0.455 0.198,0.711 0.0795 0 -0.215,0.359 0.0413 0.71 hypo +seg 5049 5051 6 0.333 0.0079,0.659 8 0.125 0,0.429 -0.208 -0 -0.509,0.156 0.0277 0.538 hypo +seg 5057 5059 4 0.75 0.343,1 7 0 0,0.312 -0.75 -0.191 -0.856,-0.191 0.00162 0.0242 hypo +seg 5128 5130 3 1 0.473,1 9 0 0,0.259 -1 -0.356 -1,-0.356 0.00028 0.00455 strongHypo +seg 5160 5162 4 1 0.549,1 11 0 0,0.221 -1 -0.45 -1,-0.45 5.52e-05 0.000733 strongHypo +seg 5162 5164 4 1 0.549,1 7 0.143 0,0.471 -0.857 -0.255 -0.88,-0.255 0.00101 0.0152 strongHypo +seg 5182 5184 3 1 0.473,1 5 0 0,0.393 -1 -0.271 -1,-0.271 0.000954 0.0179 strongHypo +seg 5192 5194 3 1 0.473,1 6 0.167 0,0.521 -0.833 -0.149 -0.858,-0.149 0.00267 0.0476 hypo +seg 5333 5335 14 0.857 0.637,1 21 0.143 0,0.316 -0.714 -0.42 -0.819,-0.42 6.9e-06 5.49e-05 strongHypo +seg 5385 5387 9 0.778 0.493,1 14 0.357 0.127,0.587 -0.421 -0.0503 -0.623,-0.0503 0.00667 0.0894 hypo +seg 5587 5589 8 1 0.717,1 18 0.778 0.581,0.975 -0.222 -0 -0.356,0.0752 0.026 0.277 hypo +seg 5857 5859 4 0.75 0.343,1 5 0.2 0,0.582 -0.55 -0 -0.745,0.0401 0.00953 0.206 hypo +seg 5886 5888 3 0.667 0.249,1 4 0.25 0,0.657 -0.417 -0 -0.685,0.196 0.0171 0.486 hypo +seg 5896 5898 3 0.667 0.249,1 4 1 0.549,1 0.333 0 -0.17,0.639 0.0214 0.429 hypo +seg 6182 6184 4 0.5 0.147,0.853 14 0.571 0.338,0.804 0.0714 0 -0.307,0.43 0.0325 1 hypo +seg 6304 6306 6 0.5 0.184,0.816 5 0 0,0.393 -0.5 -0.00245 -0.684,-0.00245 0.00849 0.182 hypo +seg 6332 6334 8 0.75 0.45,1 6 0.167 0,0.521 -0.583 -0.096 -0.751,-0.096 0.00412 0.103 hypo +seg 6403 6405 7 0.857 0.529,1 3 0 0,0.527 -0.857 -0.189 -0.87,-0.189 0.00194 0.0333 hypo +seg 6411 6413 6 1 0.652,1 4 0.75 0.343,1 -0.25 -0 -0.567,0.123 0.0255 0.4 hypo +seg 6420 6422 4 1 0.549,1 3 0.667 0.249,1 -0.333 -0 -0.639,0.17 0.0214 0.429 hypo +seg 6533 6535 3 0.667 0.249,1 14 0.0714 0,0.279 -0.595 -0.101 -0.805,-0.101 0.00412 0.0632 hypo +seg 6544 6546 4 0.75 0.343,1 15 0 0,0.171 -0.75 -0.272 -0.881,-0.272 0.000332 0.00413 strongHypo +seg 6640 6642 7 1 0.688,1 3 0.667 0.249,1 -0.333 -0 -0.669,0.0603 0.0175 0.3 hypo +seg 6654 6656 8 0.875 0.571,1 4 0.25 0,0.657 -0.625 -0.0857 -0.789,-0.0857 0.00448 0.0667 hypo +seg 6671 6673 9 0.778 0.493,1 9 0.222 0,0.507 -0.556 -0.135 -0.731,-0.135 0.00281 0.0567 hypo +seg 6732 6734 3 1 0.473,1 9 0.111 0,0.394 -0.889 -0.247 -0.889,-0.247 0.00112 0.0182 strongHypo +seg 6774 6776 6 0.833 0.479,1 7 0 0,0.312 -0.833 -0.318 -0.887,-0.318 0.000374 0.00466 strongHypo +seg 6789 6791 6 1 0.652,1 5 0 0,0.393 -1 -0.417 -1,-0.417 0.000152 0.00216 strongHypo +seg 6794 6796 9 1 0.741,1 7 0 0,0.312 -1 -0.549 -1,-0.549 8.26e-06 8.74e-05 strongHypo +seg 6839 6841 3 1 0.473,1 4 0.25 0,0.657 -0.75 -0.0327 -0.822,-0.0327 0.00572 0.143 hypo +seg 6845 6847 4 1 0.549,1 5 0.2 0,0.582 -0.8 -0.161 -0.854,-0.161 0.00238 0.0476 hypo +seg 6855 6857 4 1 0.549,1 5 0.2 0,0.582 -0.8 -0.161 -0.854,-0.161 0.00238 0.0476 hypo +seg 6861 6863 6 1 0.652,1 4 0.25 0,0.657 -0.75 -0.168 -0.85,-0.168 0.00212 0.0333 hypo +seg 6940 6942 3 1 0.473,1 3 0 0,0.527 -1 -0.17 -1,-0.17 0.00229 0.1 hypo +seg 6942 6944 4 1 0.549,1 4 0 0,0.451 -1 -0.291 -1,-0.291 0.000795 0.0286 strongHypo +seg 6950 6952 4 1 0.549,1 4 0 0,0.451 -1 -0.291 -1,-0.291 0.000795 0.0286 strongHypo +seg 6983 6985 3 1 0.473,1 5 0 0,0.393 -1 -0.271 -1,-0.271 0.000954 0.0179 strongHypo +seg 7006 7008 3 1 0.473,1 4 0 0,0.451 -1 -0.229 -1,-0.229 0.00143 0.0286 strongHypo +seg 8052 8054 4 1 0.549,1 9 0.111 0,0.394 -0.889 -0.315 -0.896,-0.315 0.0005 0.00699 strongHypo +seg 8058 8060 4 1 0.549,1 6 0.333 0.0079,0.659 -0.667 -0.0776 -0.778,-0.0776 0.00455 0.0762 hypo +seg 8089 8091 3 0.667 0.249,1 3 0 0,0.527 -0.667 -0 -0.791,0.054 0.00915 0.4 hypo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 @@ -0,0 +1,5 @@ +#chrom start end meanRatio_0 totalC_0 cSites_0 meanRatio_1 totalC_1 cSites_1 methDif_1-0 p_1_v_0 class_1_v_0 +seg 2529 2582 0.787 77 8 0.226 123 8 -0.204 3.79e-17 strongHypo +seg 2976 3065 0.833 222 3 0.241 116 3 -0.339 1.69e-22 strongHypo +seg 4327 5335 0.722 286 29 0.143 563 29 -0.201 2.3e-48 strongHypo +seg 6544 7008 0.955 86 17 0.126 97 17 -0.223 6.5e-34 strongHypo
--- a/test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr Fri Sep 06 09:54:27 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -seg 152 1305 - 20 15 5 1 -seg 2310 7008 - 95 77 18 1 -seg 8052 8091 - 3 3 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 @@ -0,0 +1,308 @@ +#chrom start end totalC_0 nominalRatio_0 ratioCI_0 totalC_1 nominalRatio_1 ratioCI_1 nominalDif_1-0 credibleDif_1-0 difCI_1-0 p_sim_1_v_0 p_fet_1_v_0 class +chr11 41 43 3 0 0,0.527 3 0 0,0.527 0 0 -0.391,0.391 0.0449 1 hypo +chr11 48 50 5 0 0,0.393 3 0 0,0.527 0 0 -0.267,0.422 0.0521 1 hypo +chr11 56 58 6 0 0,0.348 4 0 0,0.451 0 0 -0.241,0.359 0.0619 1 hypo +chr11 59 61 8 0 0,0.283 5 0.4 0.064,0.736 0.4 0.0115 0.0115,0.656 0.0099 0.128 hyper +chr11 101 103 13 0.0769 0,0.297 7 0.143 0,0.471 0.0659 0 -0.152,0.364 0.051 1 hypo +chr11 140 142 16 0 0,0.162 9 0 0,0.259 0 0 -0.107,0.216 0.123 1 hypo +chr11 144 146 14 0 0,0.181 10 0.1 0,0.364 0.1 0 -0.0722,0.317 0.0549 0.417 hypo +chr11 210 212 15 0.133 0,0.344 12 0.417 0.169,0.664 0.283 0 -0.00696,0.507 0.0139 0.185 hypo +chr11 215 217 19 0.263 0.0688,0.458 16 0.25 0.039,0.461 -0.0132 -0 -0.238,0.226 0.0566 1 hypo +chr11 316 318 24 0.0833 0,0.231 26 0.846 0.692,1 0.763 0.538 0.538,0.845 9.21e-09 3.52e-08 strongHyper +chr11 331 333 27 0.037 0,0.159 26 0.808 0.649,0.966 0.771 0.558 0.558,0.85 1.11e-09 4.05e-09 strongHyper +chr11 400 402 34 0.0588 0,0.169 34 0.412 0.254,0.57 0.353 0.18 0.18,0.486 0.000192 0.00115 hyper +chr11 407 409 33 0 0,0.0843 34 0.588 0.43,0.746 0.588 0.41 0.41,0.692 8.72e-09 3.39e-08 strongHyper +chr11 445 447 25 0.08 0,0.223 33 0.606 0.447,0.766 0.526 0.316 0.316,0.648 9.32e-06 3.59e-05 strongHyper +chr11 469 471 26 0.0385 0,0.164 34 0.588 0.43,0.746 0.55 0.352 0.352,0.661 1.43e-06 5.87e-06 strongHyper +chr11 546 548 20 0.1 0,0.271 32 0.812 0.672,0.953 0.713 0.482 0.482,0.806 1.08e-07 4.38e-07 strongHyper +chr11 666 668 20 0.05 0,0.207 38 0.553 0.401,0.704 0.503 0.29 0.29,0.612 2.88e-05 0.000144 strongHyper +chr11 694 696 22 0.318 0.132,0.504 41 0.902 0.795,1 0.584 0.368 0.368,0.716 8.72e-07 2.95e-06 strongHyper +chr11 712 714 28 0.0714 0,0.202 42 0.881 0.771,0.991 0.81 0.63 0.63,0.873 1.66e-12 4.55e-12 strongHyper +chr11 721 723 28 0.0357 0,0.153 39 0.923 0.817,1 0.887 0.719 0.719,0.926 9.44e-15 2.57e-14 strongHyper +chr11 737 739 27 0.037 0,0.159 37 0.622 0.471,0.772 0.585 0.393 0.393,0.687 2.21e-07 9.15e-07 strongHyper +chr11 753 755 23 0.087 0,0.24 41 0.78 0.653,0.908 0.694 0.488 0.488,0.783 1.74e-08 5.8e-08 strongHyper +chr11 762 764 27 0.037 0,0.159 42 0.619 0.477,0.761 0.582 0.397 0.397,0.68 1.42e-07 5.56e-07 strongHyper +chr11 792 794 37 0.324 0.178,0.471 38 0.842 0.719,0.966 0.518 0.329 0.329,0.642 1.8e-06 6.02e-06 strongHyper +chr11 798 800 36 0.306 0.159,0.452 40 0.875 0.761,0.989 0.569 0.384 0.384,0.685 1.25e-07 3.94e-07 strongHyper +chr11 816 818 33 0.0303 0,0.132 34 0.912 0.793,1 0.881 0.714 0.714,0.924 5.66e-15 1.61e-14 strongHyper +chr11 830 832 37 0.405 0.254,0.557 35 0.914 0.798,1 0.509 0.324 0.324,0.629 1.55e-06 5.05e-06 strongHyper +chr11 954 956 47 0 0,0.0605 33 0.485 0.323,0.647 0.485 0.324 0.324,0.606 1.85e-08 4.33e-08 strongHyper +chr11 977 979 47 0.255 0.132,0.379 37 0.703 0.559,0.847 0.447 0.264 0.264,0.579 1.7e-05 5.98e-05 strongHyper +chr11 1006 1008 38 0 0,0.0739 38 0.526 0.374,0.678 0.526 0.364 0.364,0.633 1.27e-08 6.16e-08 strongHyper +chr11 1066 1068 30 0.367 0.202,0.532 45 0.756 0.63,0.881 0.389 0.192 0.192,0.538 0.00027 0.00152 hyper +chr11 1116 1118 22 0.182 0.0087,0.355 35 0.771 0.632,0.911 0.59 0.362 0.362,0.713 4.09e-06 2.32e-05 strongHyper +chr11 1145 1147 18 0.556 0.345,0.766 26 0.538 0.358,0.719 -0.0171 -0 -0.248,0.222 0.0547 1 hypo +chr11 1260 1262 18 0.0556 0,0.226 24 0.375 0.192,0.558 0.319 0.0943 0.0943,0.47 0.00355 0.0264 hyper +chr11 1320 1322 17 0.118 0,0.31 25 0.64 0.461,0.819 0.522 0.26 0.26,0.661 0.000172 0.00122 strongHyper +chr11 1559 1561 36 0.194 0.0615,0.327 27 0.852 0.702,1 0.657 0.451 0.451,0.762 5.66e-08 1.9e-07 strongHyper +chr11 1574 1576 33 0.152 0.0184,0.285 28 0.607 0.435,0.779 0.456 0.245 0.245,0.601 7.43e-05 0.000388 strongHyper +chr11 1592 1594 35 0.343 0.191,0.495 33 0.697 0.544,0.85 0.354 0.149 0.149,0.509 0.001 0.00421 hyper +chr11 1609 1611 34 0.0588 0,0.169 41 0.244 0.113,0.375 0.185 0.0419 0.0419,0.305 0.0094 0.0545 hyper +chr11 1632 1634 36 0.0556 0,0.161 45 0.2 0.0811,0.319 0.144 0.0144 0.0144,0.255 0.0193 0.1 hyper +chr11 1642 1644 32 0.188 0.0468,0.328 41 0.268 0.134,0.402 0.0808 0 -0.0869,0.229 0.0606 0.578 hypo +chr11 1680 1682 34 0.0882 0,0.207 54 0.611 0.485,0.738 0.523 0.354 0.354,0.626 2.25e-07 6.09e-07 strongHyper +chr11 1689 1691 35 0.2 0.0642,0.336 51 0.471 0.338,0.603 0.271 0.095 0.095,0.408 0.00289 0.0124 hyper +chr11 1703 1705 42 0.262 0.13,0.393 49 0.755 0.635,0.875 0.493 0.319 0.319,0.614 1.06e-06 2.93e-06 strongHyper +chr11 1733 1735 43 0.512 0.368,0.655 51 0.745 0.626,0.864 0.233 0.0666 0.0666,0.379 0.00549 0.0305 hyper +chr11 1766 1768 46 0.13 0.0243,0.237 48 0.312 0.184,0.441 0.182 0.0381 0.0381,0.31 0.0105 0.0473 hyper +chr11 1869 1871 45 0.244 0.119,0.37 38 0.263 0.125,0.402 0.0187 0 -0.134,0.175 0.0834 1 hypo +chr11 2040 2042 37 0 0,0.0758 34 0 0,0.082 0 0 -0.057,0.0639 0.31 1 hypo +chr11 2104 2106 37 0.027 0,0.119 39 0.0513 0,0.149 0.0243 0 -0.0641,0.111 0.153 1 hypo +chr11 2148 2150 31 0.613 0.449,0.777 34 0.588 0.43,0.746 -0.0247 -0 -0.214,0.17 0.0664 1 hypo +chr11 2360 2362 42 0.262 0.13,0.393 26 0.538 0.358,0.719 0.277 0.0726 0.0726,0.448 0.00528 0.0373 hyper +chr11 2384 2386 34 0.382 0.226,0.539 27 0.593 0.417,0.768 0.21 0 -0.00431,0.392 0.0176 0.126 hypo +chr11 2454 2456 41 0.171 0.0504,0.291 28 0.107 0,0.246 -0.0636 -0 -0.189,0.0894 0.0753 0.729 hypo +chr11 2621 2623 9 0 0,0.259 12 0 0,0.206 0 0 -0.206,0.147 0.112 1 hypo +chr11 2648 2650 10 0 0,0.238 20 0 0,0.133 0 0 -0.202,0.0851 0.138 1 hypo +chr11 2665 2667 13 0 0,0.193 19 0.105 0,0.283 0.105 0 -0.0832,0.237 0.0587 0.502 hypo +chr11 2667 2669 17 0 0,0.153 20 0.1 0,0.271 0.1 0 -0.0533,0.233 0.057 0.489 hypo +chr11 2673 2675 13 0 0,0.193 21 0.19 0.0119,0.369 0.19 0 -0.0203,0.323 0.0228 0.144 hypo +chr11 2676 2678 17 0 0,0.153 26 0.0385 0,0.164 0.0385 0 -0.0986,0.129 0.132 1 hypo +chr11 2685 2687 16 0.0625 0,0.25 28 0.143 0,0.288 0.0804 0 -0.113,0.211 0.0661 0.638 hypo +chr11 2688 2690 19 0 0,0.139 28 0 0,0.0981 0 0 -0.114,0.0684 0.215 1 hypo +chr11 2691 2693 20 0 0,0.133 29 0.276 0.116,0.435 0.276 0.0981 0.0981,0.397 0.00242 0.0148 hyper +chr11 2713 2715 22 0 0,0.122 26 0.154 6.6e-05,0.308 0.154 0.0107 0.0107,0.277 0.0197 0.114 hyper +chr11 2723 2725 19 0 0,0.139 25 0.12 0,0.272 0.12 0 -0.0272,0.238 0.0404 0.247 hypo +chr11 2727 2729 20 0 0,0.133 20 0.35 0.153,0.547 0.35 0.143 0.143,0.501 0.000903 0.00832 hyper +chr11 2731 2733 17 0.0588 0,0.238 19 0.211 0.02,0.401 0.152 0 -0.0525,0.322 0.0341 0.342 hypo +chr11 2738 2740 18 0 0,0.146 22 0.273 0.0909,0.455 0.273 0.0783 0.0783,0.414 0.00417 0.0243 hyper +chr11 2767 2769 15 0 0,0.171 21 0.333 0.142,0.525 0.333 0.107 0.107,0.473 0.00267 0.0273 hyper +chr11 2778 2780 12 0.0833 0,0.316 22 0.455 0.261,0.648 0.371 0.0842 0.0842,0.526 0.00465 0.0527 hyper +chr11 2788 2790 8 0 0,0.283 18 0.167 0,0.359 0.167 0 -0.118,0.297 0.0398 0.529 hypo +chr11 2792 2794 7 0.143 0,0.471 22 0.318 0.132,0.504 0.175 0 -0.175,0.358 0.0341 0.635 hypo +chr11 2810 2812 3 0 0,0.527 19 0.105 0,0.283 0.105 0 -0.4,0.187 0.0515 1 hypo +chr11 2825 2827 4 0 0,0.451 15 0.133 0,0.344 0.133 0 -0.3,0.253 0.0491 1 hypo +chr11 3031 3033 13 0.0769 0,0.297 15 0.4 0.174,0.626 0.323 0.038 0.038,0.511 0.00851 0.0836 hyper +chr11 3034 3036 13 0 0,0.193 14 0.286 0.059,0.512 0.286 0.0412 0.0412,0.462 0.00859 0.0978 hyper +chr11 3052 3054 15 0.0667 0,0.264 13 0.769 0.534,1 0.703 0.377 0.377,0.816 3.11e-05 0.000267 strongHyper +chr11 3095 3097 11 0.273 0.0181,0.527 10 0.8 0.53,1 0.527 0.141 0.141,0.706 0.00253 0.03 hyper +chr11 3117 3119 12 0.0833 0,0.316 14 0.571 0.338,0.804 0.488 0.161 0.161,0.655 0.00167 0.0145 hyper +chr11 3273 3275 38 0.105 0,0.22 25 0.48 0.296,0.664 0.375 0.178 0.178,0.532 0.000337 0.00124 hyper +chr11 3283 3285 37 0.027 0,0.119 23 0.478 0.288,0.669 0.451 0.257 0.257,0.6 1.1e-05 3.67e-05 strongHyper +chr11 3323 3325 35 0.0571 0,0.165 24 0.625 0.442,0.808 0.568 0.358 0.358,0.698 8.63e-07 2.9e-06 strongHyper +chr11 3424 3426 30 0.0667 0,0.189 21 0.0952 0,0.259 0.0286 0 -0.0969,0.184 0.0956 1 hypo +chr11 3452 3454 27 0 0,0.101 17 0.588 0.374,0.803 0.588 0.349 0.349,0.729 1.79e-06 7.84e-06 strongHyper +chr11 3484 3486 25 0.04 0,0.17 18 0.556 0.345,0.766 0.516 0.275 0.275,0.667 4.33e-05 0.000196 strongHyper +chr11 3578 3580 19 0.263 0.0688,0.458 19 0.737 0.542,0.931 0.474 0.194 0.194,0.641 0.000789 0.00856 hyper +chr11 3595 3597 20 0 0,0.133 21 0.238 0.0554,0.421 0.238 0.0598 0.0598,0.385 0.00603 0.0478 hyper +chr11 3611 3613 19 0.0526 0,0.216 23 0.826 0.658,0.994 0.773 0.525 0.525,0.852 7.44e-08 3.4e-07 strongHyper +chr11 3617 3619 19 0 0,0.139 21 0.762 0.579,0.945 0.762 0.514 0.514,0.842 7.07e-08 3.39e-07 strongHyper +chr11 3639 3641 16 0.125 0,0.326 20 0.6 0.4,0.8 0.475 0.194 0.194,0.633 0.000772 0.00572 hyper +chr11 3646 3648 17 0.0588 0,0.238 23 0.391 0.204,0.579 0.332 0.0973 0.0973,0.485 0.00347 0.0257 hyper +chr11 3665 3667 13 0.0769 0,0.297 21 0.571 0.375,0.768 0.495 0.203 0.203,0.637 0.000728 0.00476 strongHyper +chr11 3672 3674 13 0 0,0.193 23 0.348 0.163,0.532 0.348 0.106 0.106,0.476 0.00296 0.0319 hyper +chr11 3677 3679 14 0 0,0.181 23 0.261 0.0841,0.438 0.261 0.0448 0.0448,0.391 0.00827 0.0645 hyper +chr11 3693 3695 17 0 0,0.153 26 0.231 0.0678,0.394 0.231 0.0451 0.0451,0.355 0.0084 0.0662 hyper +chr11 3704 3706 20 0 0,0.133 25 0.2 0.0371,0.363 0.2 0.0359 0.0359,0.329 0.0104 0.0562 hyper +chr11 3707 3709 21 0 0,0.127 25 0.16 0.00176,0.318 0.16 0.0108 0.0108,0.286 0.019 0.114 hyper +chr11 3717 3719 22 0.0455 0,0.19 21 0.286 0.0986,0.473 0.24 0.0455 0.0455,0.403 0.00857 0.0459 hyper +chr11 3960 3962 21 0 0,0.127 18 0.167 0,0.359 0.167 0.011 0.011,0.326 0.0188 0.0893 hyper +chr11 3991 3993 20 0 0,0.133 24 0.167 0.00373,0.33 0.167 0.0109 0.0109,0.296 0.0184 0.114 hyper +chr11 4056 4058 22 0 0,0.122 24 0.292 0.115,0.468 0.292 0.111 0.111,0.431 0.0016 0.00965 hyper +chr11 4163 4165 26 0.0769 0,0.215 30 0.0333 0,0.144 -0.0436 -0 -0.167,0.067 0.103 0.592 hypo +chr11 4195 4197 23 0.0435 0,0.183 26 0.231 0.0678,0.394 0.187 0.0142 0.0142,0.331 0.0161 0.103 hyper +chr11 4202 4204 21 0 0,0.127 30 0.0667 0,0.189 0.0667 0 -0.056,0.159 0.09 0.506 hypo +chr11 4207 4209 18 0.0556 0,0.226 31 0.194 0.0495,0.338 0.138 0 -0.0495,0.266 0.0376 0.238 hypo +chr11 4243 4245 30 0.133 0,0.271 27 0.111 0,0.254 -0.0222 -0 -0.164,0.129 0.0905 1 hypo +chr11 4248 4250 32 0.0312 0,0.136 31 0.0323 0,0.14 0.00101 0 -0.0916,0.0963 0.165 1 hypo +chr11 4284 4286 34 0.0882 0,0.207 31 0.226 0.0775,0.374 0.138 0 -0.014,0.281 0.0299 0.174 hypo +chr11 4289 4291 33 0 0,0.0843 27 0.0741 0,0.208 0.0741 0 -0.0153,0.186 0.0629 0.198 hypo +chr11 4302 4304 34 0 0,0.082 30 0 0,0.0921 0 0 -0.0611,0.0723 0.285 1 hypo +chr11 4307 4309 31 0 0,0.0894 34 0.0294 0,0.129 0.0294 0 -0.0497,0.107 0.175 1 hypo +chr11 4314 4316 27 0 0,0.101 33 0.0606 0,0.174 0.0606 0 -0.0384,0.149 0.094 0.497 hypo +chr11 4320 4322 25 0.04 0,0.17 34 0.0882 0,0.207 0.0482 0 -0.082,0.153 0.0995 0.63 hypo +chr11 4330 4332 23 0 0,0.117 36 0.0278 0,0.122 0.0278 0 -0.0768,0.0958 0.177 1 hypo +chr11 4340 4342 22 0.0455 0,0.19 31 0.0323 0,0.14 -0.0132 -0 -0.143,0.0832 0.134 1 hypo +chr11 4365 4367 20 0 0,0.133 33 0.0303 0,0.132 0.0303 0 -0.0885,0.103 0.162 1 hypo +chr11 4393 4395 18 0 0,0.146 28 0.143 0,0.288 0.143 0 -0.0153,0.253 0.0296 0.144 hypo +chr11 4403 4405 16 0 0,0.162 25 0 0,0.109 0 0 -0.133,0.0747 0.19 1 hypo +chr11 4405 4407 17 0 0,0.153 24 0 0,0.113 0 0 -0.125,0.0796 0.193 1 hypo +chr11 4420 4422 14 0.0714 0,0.279 22 0.136 0,0.304 0.0649 0 -0.145,0.216 0.0682 1 hypo +chr11 4456 4458 14 0 0,0.181 15 0 0,0.171 0 0 -0.14,0.128 0.149 1 hypo +chr11 4458 4460 14 0 0,0.181 16 0.0625 0,0.25 0.0625 0 -0.101,0.206 0.0874 1 hypo +chr11 4469 4471 14 0.0714 0,0.279 13 0.154 0,0.385 0.0824 0 -0.132,0.291 0.0559 0.596 hypo +chr11 4482 4484 15 0.0667 0,0.264 19 0 0,0.139 -0.0667 -0 -0.228,0.0612 0.0804 0.441 hypo +chr11 4499 4501 16 0.0625 0,0.25 24 0.0417 0,0.176 -0.0208 -0 -0.189,0.102 0.101 1 hypo +chr11 4519 4521 19 0.105 0,0.283 23 0.304 0.123,0.485 0.199 0 -0.019,0.37 0.021 0.149 hypo +chr11 4523 4525 20 0.05 0,0.207 25 0.28 0.108,0.452 0.23 0.0331 0.0331,0.378 0.0106 0.0592 hyper +chr11 4532 4534 20 0 0,0.133 23 0.174 0.00602,0.342 0.174 0.0155 0.0155,0.308 0.0166 0.111 hyper +chr11 4549 4551 21 0.0476 0,0.198 26 0.231 0.0678,0.394 0.183 0.00182 0.00182,0.327 0.0191 0.112 hyper +chr11 4558 4560 21 0 0,0.127 25 0.2 0.0371,0.363 0.2 0.0399 0.0399,0.33 0.00952 0.0536 hyper +chr11 4588 4590 21 0.0476 0,0.198 15 0 0,0.171 -0.0476 -0 -0.159,0.105 0.11 1 hypo +chr11 4594 4596 20 0 0,0.133 18 0.0556 0,0.226 0.0556 0 -0.0646,0.193 0.0964 0.474 hypo +chr11 4633 4635 15 0.0667 0,0.264 19 0.263 0.0688,0.458 0.196 0 -0.0347,0.369 0.0237 0.196 hypo +chr11 4692 4694 15 0.0667 0,0.264 16 0.188 0,0.396 0.121 0 -0.0941,0.308 0.0454 0.6 hypo +chr11 4723 4725 16 0 0,0.162 17 0.235 0.0315,0.439 0.235 0.0328 0.0328,0.398 0.0105 0.103 hyper +chr11 4744 4746 15 0.0667 0,0.264 21 0.0952 0,0.259 0.0286 0 -0.161,0.177 0.0837 1 hypo +chr11 4756 4758 19 0 0,0.139 24 0.208 0.0409,0.376 0.208 0.0368 0.0368,0.34 0.0101 0.0562 hyper +chr11 4785 4787 19 0.0526 0,0.216 22 0.182 0.0087,0.355 0.129 0 -0.0537,0.284 0.0407 0.35 hypo +chr11 4789 4791 21 0.0476 0,0.198 24 0.0833 0,0.231 0.0357 0 -0.11,0.167 0.0974 1 hypo +chr11 4791 4793 21 0.19 0.0119,0.369 23 0.261 0.0841,0.438 0.0704 0 -0.139,0.262 0.0571 0.724 hypo +chr11 4799 4801 24 0.0833 0,0.231 25 0 0,0.109 -0.0833 -0 -0.203,0.0283 0.0616 0.235 hypo +chr11 4845 4847 24 0.0417 0,0.176 23 0 0,0.117 -0.0417 -0 -0.147,0.063 0.127 1 hypo +chr11 4860 4862 24 0 0,0.113 17 0 0,0.153 0 0 -0.0796,0.125 0.193 1 hypo +chr11 4869 4871 24 0 0,0.113 21 0.238 0.0554,0.421 0.238 0.0726 0.0726,0.39 0.00403 0.0167 hyper +chr11 4872 4874 26 0 0,0.105 20 0.1 0,0.271 0.1 0 -0.0148,0.243 0.0448 0.184 hypo +chr11 4894 4896 25 0 0,0.109 24 0.0833 0,0.231 0.0833 0 -0.0283,0.203 0.0616 0.235 hypo +chr11 4908 4910 26 0.0385 0,0.164 27 0.0741 0,0.208 0.0356 0 -0.0867,0.155 0.109 1 hypo +chr11 4923 4925 26 0 0,0.105 28 0 0,0.0981 0 0 -0.0815,0.0739 0.249 1 hypo +chr11 4942 4944 25 0 0,0.109 22 0.136 0,0.304 0.136 0.00635 0.00635,0.275 0.0239 0.095 hyper +chr11 5009 5011 21 0.0476 0,0.198 25 0.08 0,0.223 0.0324 0 -0.113,0.16 0.101 1 hypo +chr11 5015 5017 19 0.0526 0,0.216 28 0.107 0,0.246 0.0545 0 -0.109,0.179 0.0842 0.638 hypo +chr11 5025 5027 20 0.05 0,0.207 26 0.192 0.0338,0.351 0.142 0 -0.0356,0.283 0.034 0.212 hypo +chr11 5036 5038 16 0.125 0,0.326 25 0.04 0,0.17 -0.085 -0 -0.266,0.057 0.0592 0.55 hypo +chr11 5047 5049 17 0 0,0.153 22 0 0,0.122 0 0 -0.123,0.088 0.188 1 hypo +chr11 5051 5053 14 0 0,0.181 21 0.0476 0,0.198 0.0476 0 -0.115,0.157 0.109 1 hypo +chr11 5053 5055 16 0 0,0.162 21 0 0,0.127 0 0 -0.13,0.0914 0.179 1 hypo +chr11 5097 5099 20 0 0,0.133 24 0 0,0.113 0 0 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6491 6493 25 0.04 0,0.17 18 0.278 0.0771,0.478 0.238 0.0497 0.0497,0.416 0.00794 0.0672 hyper +chr11 6526 6528 35 0.0286 0,0.125 26 0.115 0,0.263 0.0868 0 -0.0247,0.219 0.0549 0.303 hypo +chr11 6560 6562 25 0.24 0.0727,0.407 30 0.233 0.0816,0.385 -0.00667 -0 -0.195,0.173 0.0714 1 hypo +chr11 6596 6598 38 0.421 0.27,0.572 30 0.6 0.433,0.767 0.179 0 -0.0236,0.356 0.0237 0.222 hypo +chr11 6730 6732 41 0.366 0.223,0.509 31 0.516 0.349,0.683 0.15 0 -0.0438,0.327 0.0316 0.236 hypo +chr11 6857 6859 33 0.212 0.0704,0.354 46 0.239 0.116,0.362 0.027 0 -0.135,0.173 0.0826 1 hypo +chr11 6900 6902 29 0.862 0.72,1 46 0.804 0.687,0.921 -0.0577 -0 -0.187,0.0999 0.0766 0.755 hypo +chr11 6902 6904 29 0.483 0.311,0.655 46 0.804 0.687,0.921 0.322 0.132 0.132,0.479 0.00124 0.00524 hyper +chr11 6979 6981 25 0.28 0.108,0.452 39 0.487 0.337,0.638 0.207 0 -0.00347,0.377 0.0177 0.123 hypo +chr11 7085 7087 26 0.346 0.172,0.521 27 0.704 0.537,0.871 0.358 0.124 0.124,0.528 0.00216 0.0135 hyper +chr11 7166 7168 19 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-0.0523,0.15 0.126 0.48 hypo +chr11 8786 8788 25 0 0,0.109 19 0 0,0.139 0 0 -0.0781,0.112 0.207 1 hypo +chr11 8812 8814 22 0.0909 0,0.249 21 0 0,0.127 -0.0909 -0 -0.217,0.038 0.0592 0.488 hypo +chr11 8829 8831 20 0 0,0.133 22 0.136 0,0.304 0.136 0 -0.0114,0.27 0.0304 0.233 hypo +chr11 8836 8838 21 0 0,0.127 21 0.0476 0,0.198 0.0476 0 -0.0664,0.167 0.112 1 hypo +chr11 8855 8857 17 0.0588 0,0.238 22 0.0909 0,0.249 0.0321 0 -0.14,0.174 0.0887 1 hypo +chr11 8902 8904 17 0 0,0.153 15 0.333 0.111,0.555 0.333 0.104 0.104,0.508 0.00262 0.0149 hyper +chr11 8914 8916 20 0.35 0.153,0.547 13 0.308 0.0724,0.543 -0.0423 -0 -0.281,0.229 0.0495 1 hypo +chr11 8920 8922 22 0 0,0.122 12 0 0,0.206 0 0 -0.0801,0.173 0.157 1 hypo +chr11 8948 8950 33 0 0,0.0843 17 0.0588 0,0.238 0.0588 0 -0.0234,0.214 0.0814 0.34 hypo +chr11 8975 8977 42 0.0476 0,0.139 19 0 0,0.139 -0.0476 -0 -0.11,0.0832 0.131 1 hypo +chr11 9127 9129 41 0.0244 0,0.108 31 0.0968 0,0.225 0.0724 0 -0.0228,0.187 0.0662 0.308 hypo +chr11 9136 9138 42 0.0476 0,0.139 33 0.0606 0,0.174 0.013 0 -0.0771,0.12 0.143 1 hypo +chr11 9227 9229 45 0.0444 0,0.131 38 0.0526 0,0.153 0.00819 0 -0.0754,0.103 0.16 1 hypo +chr11 9270 9272 40 0.025 0,0.111 33 0.0909 0,0.213 0.0659 0 -0.0287,0.175 0.0758 0.322 hypo +chr11 9301 9303 40 0.175 0.0523,0.298 33 0.0303 0,0.132 -0.145 -0.0191 -0.253,-0.0191 0.0174 0.0652 hypo +chr11 9371 9373 25 0 0,0.109 32 0 0,0.0868 0 0 -0.0872,0.0628 0.257 1 hypo +chr11 9380 9382 25 0.04 0,0.17 31 0 0,0.0894 -0.04 -0 -0.147,0.0405 0.129 0.446 hypo +chr11 9447 9449 17 0 0,0.153 30 0 0,0.0921 0 0 -0.129,0.0611 0.207 1 hypo +chr11 9478 9480 16 0 0,0.162 21 0.0476 0,0.198 0.0476 0 -0.097,0.16 0.111 1 hypo +chr11 9510 9512 14 0 0,0.181 23 0.0435 0,0.183 0.0435 0 -0.119,0.143 0.117 1 hypo +chr11 9588 9590 20 0 0,0.133 18 0.111 0,0.296 0.111 0 -0.0292,0.261 0.0448 0.218 hypo +chr11 9677 9679 11 0.0909 0,0.339 13 0.231 0,0.466 0.14 0 -0.131,0.354 0.0398 0.596 hypo +chr11 9697 9699 14 0 0,0.181 15 0.2 0,0.417 0.2 0 -0.00842,0.371 0.02 0.224 hypo +chr11 9709 9711 11 0 0,0.221 18 0.111 0,0.296 0.111 0 -0.104,0.245 0.0574 0.512 hypo +chr11 9729 9731 6 0.167 0,0.521 16 0 0,0.162 -0.167 -0 -0.475,0.0224 0.0282 0.273 hypo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 @@ -0,0 +1,2 @@ +#chrom start end meanRatio_0 totalC_0 cSites_0 meanRatio_1 totalC_1 cSites_1 methDif_1-0 p_1_v_0 class_1_v_0 +chr11 316 1705 0.148 1061 35 0.657 1278 35 0.326 3.11e-141 strongHyper