| Previous changeset 5:715d03e1fd83 (2017-03-20) Next changeset 7:f9486b344dbc (2017-04-25) |
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Commit message:
Uploaded |
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modified:
findDMR/findDMR.R findDMR/findDMR.xml |
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added:
findDMR/test-data/DMRs.txt |
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removed:
findDMR/.Rhistory findDMR/test-data/._input.csv findDMR/test-data/DMR.bed findDMR/test-data/MetaTable.csv findDMR/test-data/input.csv findDMR/tool_dependencies.xml |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/.Rhistory --- a/findDMR/.Rhistory Mon Mar 20 06:51:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -clusterSize=2 -class(clusterSize) -type(clusterSize) |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/findDMR.R --- a/findDMR/findDMR.R Mon Mar 20 06:51:59 2017 -0400 +++ b/findDMR/findDMR.R Tue Apr 25 13:19:29 2017 -0400 |
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| @@ -1,45 +1,22 @@ +require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE) +require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE) require("minfi", quietly = TRUE) -require("ChIPseeker", quietly = TRUE) -require("ChIPpeakAnno", quietly = TRUE) -require("data.table", quietly = TRUE) +options(warn = -1) +options("download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) -GSMTable = args[1] -platform = args[2] -Data_Table = args[3] -cutoff = as.numeric(args[4]) -clusterSize = as.numeric(args[5]) -DMR = args[6] -TAB = fread(GSMTable) - -IlmnInfo = fread(platform) +input1 = args[1] +input2 = args[2] +output = args[3] -gmSet = fread(Data_Table) - -# bumphunter Run with processed data -designMatrix <- model.matrix( ~ TAB$Phenotype) +GRset <- get(load(input1)) -bumps <- bumphunter( - as.matrix(gmSet), - design = designMatrix, - pos = IlmnInfo$BP, - cutoff = cutoff, - chr = IlmnInfo$CHR -) +pheno <- fread(input2) + +designMatrix <- model.matrix(~ pheno$Phenotype) -# choose DMR's of a certain length threshold -DMRTable <- bumps$table[which(bumps$table$L >= clusterSize), ] -DMRInfo <- data.table(DMRTable$chr, DMRTable$start, DMRTable$end) - - - -write.table( - DMRInfo, - DMR, - quote = F, - sep = "\t", - row.names = F, - col.names = F -) +dmrs <- bumphunter(GRset, design = designMatrix, + cutoff = 0.2, B=0, type="Beta") +write.table(dmrs, output) |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/findDMR.xml --- a/findDMR/findDMR.xml Mon Mar 20 06:51:59 2017 -0400 +++ b/findDMR/findDMR.xml Tue Apr 25 13:19:29 2017 -0400 |
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| @@ -1,56 +1,35 @@ -<tool id="DMR" name="findDMR" version="1.16.2"> - <description> -from series of samples - </description> +<tool id="findDMR" name="findDMR" version="1.16.2"> <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> + <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement> +</requirements> <stdio> <exit_code range="1:" /> </stdio> - <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> + <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command> <inputs> - <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> - <validator type="empty_field" message="This field is required."/> - </param> - <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> - <validator type="empty_field" message="This field is required."/> - </param> - <param name="cutoff" type="float" value="" - label="Enter cutoff size (number)" - help="e.g. '0.2'" > - </param> - <param name="clusterSize" type="float" value="" - label="Enter cluster size (number)" - help="e.g. '2'" > - </param> + <param name="input1" format="Rdata"label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/> + <param name="input2" format="txt"label="PhenoTab.txt" help="ID and Phenotype table"/> </inputs> <outputs> - <data format="bed" name="DMR" label="DMR.bed"/> + <data format="txt" name="output" label="findDMR.txt"/> </outputs> <tests> <test> <param name="test"> <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.txt"/> - <element name="platform" value="test-data/platform.txt"/> - <element name="Data_Table" value="test-data/Data_Table.txt"/> - <element name="cutoff" value="0.2"/> - <element name="clusterSize" value="2"/> + <collection type="data"> + <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/> + <element format="txt" name="input2" label="test-data/PhenoTab.txt"/> </collection> </element> </param> - <output format="bed" name="DMR" label="test-data/DMR.bed"/> + <output format="txt" name="output" label="test-data/findDMR.txt"/> </test> </tests> <help> -**Description** +Identify CpGs where methylation is associated with a continuous or categorical phenotype. </help> <citations> -DMR +Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369. </citations> </tool> |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/test-data/._input.csv |
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| Binary file findDMR/test-data/._input.csv has changed |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/test-data/DMR.bed --- a/findDMR/test-data/DMR.bed Mon Mar 20 06:51:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,9881 +0,0 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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/test-data/DMRs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/test-data/DMRs.txt Tue Apr 25 13:19:29 2017 -0400 |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/test-data/MetaTable.csv --- a/findDMR/test-data/MetaTable.csv Mon Mar 20 06:51:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
| b |
| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/test-data/input.csv --- a/findDMR/test-data/input.csv Mon Mar 20 06:51:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
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| diff -r 715d03e1fd83 -r a0e3f4efb03f findDMR/tool_dependencies.xml --- a/findDMR/tool_dependencies.xml Mon Mar 20 06:51:59 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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