| Previous changeset 32:be1ca0e7829b (2017-04-13) Next changeset 34:59a5237b72a3 (2017-04-14) |
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Commit message:
Uploaded |
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added:
findDMR/.Rhistory findDMR/._.DS_Store findDMR/findDMR.R findDMR/findDMR.xml findDMR/test-data/._.DS_Store 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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removed:
GRsetFromGEO/._.DS_Store GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/test-data/GenomicRatioSet.Rdata GRsetFromGEO/tool_dependencies.xml |
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| diff -r be1ca0e7829b -r 2c799524e1d3 GRsetFromGEO/._.DS_Store |
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| Binary file GRsetFromGEO/._.DS_Store has changed |
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| diff -r be1ca0e7829b -r 2c799524e1d3 GRsetFromGEO/GRsetFromGEO.R --- a/GRsetFromGEO/GRsetFromGEO.R Thu Apr 13 12:50:58 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -require("minfi", quietly = TRUE) - -args <- commandArgs(trailingOnly = TRUE) -GSE = args[1] -output = args[2] - -GRset <- getGenomicRatioSetFromGEO(GSE) - -#save(GRset,output) -a<-"franek" - -write.table(a, output, row.names = FALSE,quote=FALSE,sep="\t") \ No newline at end of file |
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| diff -r be1ca0e7829b -r 2c799524e1d3 GRsetFromGEO/GRsetFromGEO.xml --- a/GRsetFromGEO/GRsetFromGEO.xml Thu Apr 13 12:50:58 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,33 +0,0 @@ -<tool id="GRset" name="GRsetFromGEO" version="1.16.2"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> -</stdio> - <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> - <inputs> - <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> - </inputs> - <outputs> - <data format="txt" name="output" label="GSMTable.txt"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSE" value="GSE51547"/> - </collection> - </element> - </param> - <output format="txt" name="output" label="test-data/GSMTable.txt"/> - </test> - </tests> - <help> -Reading Illumina methylation array data from GEO. -</help> -<citations> -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 be1ca0e7829b -r 2c799524e1d3 GRsetFromGEO/test-data/GenomicRatioSet.Rdata |
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| Binary file GRsetFromGEO/test-data/GenomicRatioSet.Rdata has changed |
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| diff -r be1ca0e7829b -r 2c799524e1d3 GRsetFromGEO/tool_dependencies.xml --- a/GRsetFromGEO/tool_dependencies.xml Thu Apr 13 12:50:58 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,274 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\' ?>\n-<tool_dependency>\n- <actions>\n- <action type="setup_r_environment">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n- <package name="R" version="3.2.1"/>\n- </repository>\n- <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n- https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n- </package>\n- <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n- https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n- </package>\n- <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n- https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n- </package>\n- <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n- https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n- 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file\n' |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/.Rhistory Fri Apr 14 06:44:35 2017 -0400 |
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| @@ -0,0 +1,3 @@ +clusterSize=2 +class(clusterSize) +type(clusterSize) |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/._.DS_Store |
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| Binary file findDMR/._.DS_Store has changed |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/findDMR.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/findDMR.R Fri Apr 14 06:44:35 2017 -0400 |
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| @@ -0,0 +1,45 @@ +require("minfi", quietly = TRUE) +require("ChIPseeker", quietly = TRUE) +require("ChIPpeakAnno", quietly = TRUE) +require("data.table", quietly = TRUE) + + +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) + +gmSet = fread(Data_Table) + +# bumphunter Run with processed data +designMatrix <- model.matrix( ~ TAB$Phenotype) + +bumps <- bumphunter( + as.matrix(gmSet), + design = designMatrix, + pos = IlmnInfo$BP, + cutoff = cutoff, + chr = IlmnInfo$CHR +) + +# 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 +) |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/findDMR.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/findDMR.xml Fri Apr 14 06:44:35 2017 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="DMR" name="findDMR" version="1.16.2"> + <description> +from series of samples + </description> + <requirements> + <requirement 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> + <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> + </inputs> + <outputs> + <data format="bed" name="DMR" label="DMR.bed"/> + </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> + </element> + </param> + <output format="bed" name="DMR" label="test-data/DMR.bed"/> + </test> + </tests> + <help> +**Description** +</help> +<citations> +DMR +</citations> +</tool> |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/test-data/._input.csv |
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| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/test-data/DMR.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/test-data/DMR.bed Fri Apr 14 06:44:35 2017 -0400 |
| b |
| b'@@ -0,0 +1,9881 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|
| b |
| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/test-data/MetaTable.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/test-data/MetaTable.csv Fri Apr 14 06:44:35 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +"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 be1ca0e7829b -r 2c799524e1d3 findDMR/test-data/input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/test-data/input.csv Fri Apr 14 06:44:35 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +ID,Phenotype +GSM1247787,melanoma +GSM1247784,melanoma +GSM1247733,healthy |
| b |
| diff -r be1ca0e7829b -r 2c799524e1d3 findDMR/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findDMR/tool_dependencies.xml Fri Apr 14 06:44:35 2017 -0400 |
| b |
| b'@@ -0,0 +1,273 @@\n+<?xml version="1.0"?>\n+<tool_dependency>\n+ <install version="1.0">\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1"/>\n+ </repository>\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n+ https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n+ </package>\n+ <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n+ https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n+ </package>\n+ <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n+ 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