| Previous changeset 1:9d1256d9ef0b (2017-06-11) Next changeset 3:783e8b70b047 (2018-09-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a |
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modified:
goseq.r goseq.xml test-data/wal.tab |
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added:
test-data/dge_list_zf.tab test-data/gene_length_zf.tab test-data/getgo.danRer10.tab test-data/getgo.hg38.tab test-data/goseq_analysis.RData test-data/length_bias_plot.pdf test-data/nobias.tab test-data/samp.tab test-data/sample_vs_wallenius_plot.pdf |
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removed:
test-data/gc.tab test-data/go_terms.tab test-data/length.tab |
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| diff -r 9d1256d9ef0b -r ab492df30cdf goseq.r --- a/goseq.r Sun Jun 11 08:57:39 2017 -0400 +++ b/goseq.r Mon Oct 23 11:19:12 2017 -0400 |
| [ |
| @@ -11,8 +11,8 @@ option_list <- list( make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"), make_option(c("-w","--wallenius_tab"), type="character", help="Path to output file with P-values estimated using wallenius distribution."), - make_option(c("-s","--sampling_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution."), - make_option(c("-n","--nobias_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution and no correction for gene length bias."), + make_option(c("-s","--sampling_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using sampling distribution."), + make_option(c("-n","--nobias_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using hypergeometric distribution and no correction for gene length bias."), make_option(c("-l","--length_bias_plot"), type="character", default=FALSE, help="Path to length-bias plot."), make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."), make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"), @@ -23,7 +23,9 @@ make_option(c("-p", "--p_adj_method"), default="BH", type="character", help="Multiple hypothesis testing correction method to use"), make_option(c("-cat", "--use_genes_without_cat"), default=FALSE, type="logical", help="A large number of gene may have no GO term annotated. If this option is set to FALSE, genes without category will be ignored in the calculation of p-values(default behaviour). If TRUE these genes will count towards the total number of genes outside the tested category (default behaviour prior to version 1.15.2)."), - make_option(c("-plots", "--make_plots"), default=FALSE, type="logical", help="produce diagnostic plots?") + make_option(c("-plots", "--make_plots"), default=FALSE, type="logical", help="produce diagnostic plots?"), + make_option(c("-fc", "--fetch_cats"), default=NULL, type="character", help="Categories to get can include one or more of GO:CC, GO:BP, GO:MF, KEGG"), + make_option(c("-rd", "--rdata"), default=NULL, type="character", help="Path to RData output file.") ) parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) @@ -44,15 +46,27 @@ p_adj_method = args$p_adj_method use_genes_without_cat = args$use_genes_without_cat make_plots = args$make_plots +rdata = args$rdata + +if (!is.null(args$fetch_cats)) { + fetch_cats = unlist(strsplit(args$fetch_cats, ",")) +} # format DE genes into named vector suitable for goseq -dge_table = read.delim(dge_file, header = FALSE, sep="\t") +# check if header is present +first_line = read.delim(dge_file, header = FALSE, nrow=1) +second_col = toupper(first_line[, ncol(first_line)]) +if (second_col == TRUE || second_col == FALSE) { + dge_table = read.delim(dge_file, header = FALSE, sep="\t") +} else { + dge_table = read.delim(dge_file, header = TRUE, sep="\t") +} genes = as.numeric(as.logical(dge_table[,ncol(dge_table)])) # Last column contains TRUE/FALSE names(genes) = dge_table[,1] # Assuming first column contains gene names # gene lengths, assuming last column if (length_file != "FALSE" ) { - first_line = read.delim(dge_file, header = FALSE, nrow=1) + first_line = read.delim(length_file, header = FALSE, nrow=1) if (is.numeric(first_line[, ncol(first_line)])) { length_table = read.delim(length_file, header=FALSE, sep="\t", check.names=FALSE) } else { @@ -66,7 +80,7 @@ # Estimate PWF -if (make_plots == TRUE) { +if (make_plots != 'false') { pdf(length_bias_plot) } pwf=nullp(genes, genome = genome, id = gene_id, bias.data = gene_lengths, plot.fit=make_plots) @@ -74,7 +88,7 @@ # Fetch GO annotations if category_file hasn't been supplied: if (category_file == "FALSE") { - go_map=getgo(genes = names(genes), genome = genome, id = gene_id, fetch.cats=c("GO:CC", "GO:BP", "GO:MF", "KEGG")) + go_map=getgo(genes = names(genes), genome=genome, id=gene_id, fetch.cats=fetch_cats) } else { # check for header: first entry in first column must be present in genes, else it's a header first_line = read.delim(category_file, header = FALSE, nrow=1) @@ -103,7 +117,13 @@ # Sampling distribution if (repcnt > 0) { + + # capture the sampling progress so it doesn't fill stdout + zz <- file("/dev/null", open = "wt") + sink(zz) GO.samp=goseq(pwf, genome = genome, id = gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map) + sink() + GO.samp$p.adjust.over_represented = p.adjust(GO.samp$over_represented_pvalue, method=p_adj_method) GO.samp$p.adjust.under_represented = p.adjust(GO.samp$under_represented_pvalue, method=p_adj_method) write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) @@ -118,4 +138,10 @@ } } +# Output RData file +if (!is.null(args$rdata)) { + save.image(file = "goseq_analysis.RData") +} + + sessionInfo() |
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| diff -r 9d1256d9ef0b -r ab492df30cdf goseq.xml --- a/goseq.xml Sun Jun 11 08:57:39 2017 -0400 +++ b/goseq.xml Mon Oct 23 11:19:12 2017 -0400 |
| [ |
| b'@@ -1,8 +1,12 @@\n-<tool id="goseq" name="goseq" version="0.2.2">\n+<tool id="goseq" name="goseq" version="1.26.0">\n <description>tests for overrepresented gene categories</description>\n <requirements>\n <requirement type="package" version="1.3.2">r-optparse</requirement>\n- <requirement type="package" version="1.22.0">bioconductor-goseq</requirement>\n+ <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>\n+ <requirement type="package" version="3.3.0">bioconductor-org.hs.eg.db</requirement>\n+ <requirement type="package" version="3.4.0">bioconductor-org.dm.eg.db</requirement>\n+ <requirement type="package" version="3.4.1">bioconductor-org.dr.eg.db</requirement>\n+ <requirement type="package" version="3.4.0">bioconductor-org.mm.eg.db</requirement>\n </requirements>\n <stdio>\n <regex match="Execution halted"\n@@ -18,122 +22,334 @@\n level="fatal"\n description="An undefined error occured, please check your input carefully and contact your administrator." />\n </stdio>\n+ <version_command><![CDATA[\n+echo $(R --version | grep version | grep -v GNU)", goseq version" $(R --vanilla --slave -e "library(goseq); cat(sessionInfo()\\$otherPkgs\\$goseq\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\\$otherPkgs\\$optparse\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\\$otherPkgs\\$org.Hs.eg.db\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dr.eg.db version" $(R --vanilla --slave -e "library(org.Dr.eg.db); cat(sessionInfo()\\$otherPkgs\\$org.Dr.eg.db\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Dm.eg.db version" $(R --vanilla --slave -e "library(org.Dm.eg.db); cat(sessionInfo()\\$otherPkgs\\$org.Dm.eg.db\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\\$otherPkgs\\$org.Mm.eg.db\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+ ]]></version_command>\n <command><![CDATA[\n- Rscript \'$__tool_directory__\'/goseq.r --dge_file \'$dge_file\'\n- --length_file \'$length_file\'\n- --category_file \'$category_file\'\n- #if $methods[\'wallenius\']:\n- --wallenius_tab \'$wallenius_tab\'\n- #end if\n- #if $methods[\'hypergeometric\']:\n- --nobias_tab \'$nobias_tab\'\n- #end if\n- --repcnt \'$methods.repcnt\'\n- --sampling_tab \'$sampling_tab\'\n- --p_adj_method \'$p_adj_method\'\n- --use_genes_without_cat \'$use_genes_without_cat\'\n- --make_plots \'$make_plots\'\n- --length_bias_plot \'$length_bias_plot\'\n- --sample_vs_wallenius_plot \'$sample_vs_wallenius_plot\'\n+Rscript \'$__tool_directory__/goseq.r\'\n+\n+--dge_file \'$dge_file\'\n+--length_file \'$length_file\'\n+\n+#if $categorySource.catSource == \'getgo\':\n+ --genome $categorySource.genome\n+ --gene_id $categorySource.gene_id\n+ --fetch_cats \'$categorySource.fetchcats\'\n+#elif $categorySource.catSource == \'history\':\n+ --category_file \'$categorySource.category_file\'\n+#end if\n+\n+#if $methods[\'wallenius\']:\n+ --wallenius_tab \'$wallenius_tab\'\n+#end if\n+#if $methods[\'hypergeometric\']:\n+ --nobias_tab \'$nobias_tab\'\n+#end if\n+--repcnt \'$methods.repcnt\'\n+--sampling_tab \'$sampling_tab\'\n+\n+--make_plots \'$out.make_plots\'\n+--length_bias_plot \'$length_bias_plot\'\n+--sample_vs_wallenius_plot \'$sample_vs_wallenius_plot\'\n+--rdata \'$out.rdata_out\'\n+\n+--p_adj_method \'$adv.p_adj_method\'\n+--use_genes_without_cat \'$adv.use_genes_without_cat\'\n+\n ]]></command>\n+\n+ <!-- Input Files-->\n <inputs>\n- <param name="dge_file" help="A tabular file with gene names in the first column, and TRUE or FALSE in the last column. TRUE means a gene is differentially expressed. See help section for details." label="Differentially expressed gene file" t'..b'e Wallenius approximation. This is easily accomplished by using the method option to additionally specify sampling and the number of samples to generate.\n+\n+*Hypergeometric*\n+\n+assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution (no length bias correction is performed). Useful if you wish to test the effect of length bias on your results.\n+Caution: Hypergeometric should NEVER be used for producing results for biological interpretation of RNA-seq data. If length bias is truly not present in your data, goseq will produce a nearly flat PWF plot, no length bias correction will be applied to your data, and all methods will produce the same results.\n \n- *"Sampling"* uses random sampling to approximate the true distribution and uses it to calculate the p-values for over (and under) representation of categories.\n- Although this is the most accurate method given a high enough value of sampling depth, its use quickly becomes computationally prohibitive.\n+-----\n+\n+**More Information**\n \n- *"Hypergeometric"* assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution.\n- Useful if you wish to test the effect of selection bias on your results.\n+In order to account for the length bias inherent to RNA-seq data when performing a GO analysis\n+(or other category based tests), one cannot simply use the hypergeometric distribution as the null\n+distribution for category membership, which is appropriate for data without DE length bias, such\n+as microarray data. GO analysis of RNA-seq data requires the use of random sampling in order\n+to generate a suitable null distribution for GO category membership and calculate each categories\n+significance for over representation amongst DE genes.\n+\n+However, this random sampling is computationally expensive. In most cases, the Wallenius\n+distribution can be used to approximate the true null distribution, without any significant loss in\n+accuracy. The goseq package implements this approximation as its default option. The option\n+to generate the null distribution using random sampling is also included as an option, but users\n+should be aware that the default number of samples generated will not be enough to accurately\n+call enrichment when there are a large number of go terms.\n \n- CAUTION: "Hypergeometric" should NEVER be used for producing results for biological interpretation.\n- If there is genuinely no bias in power to detect DE in your experiment, the PWF will reflect this and the other methods will produce accuracte results.\n+Having established a null distribution, each category is then tested for over and under\n+representation amongst the set of differentially expressed genes and the null is used to calculate a\n+p-value for under and over representation.\n+\n+Having performed a GO analysis, you may now wish to interpret the results. If you wish to\n+identify categories significantly enriched/unenriched below some p-value cutoff, it is necessary to\n+first apply some kind of multiple hypothesis testing correction. For example, you can identify GO categories over\n+enriched using a 0.05 FDR (p.adjust) cutoff [Benjamini and Hochberg, 1995].\n \n- .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf\n+Unless you are a machine, GO and KEGG category identifiers are probably not very meaningful to you.\n+Information about each identifier can be obtained from the `Gene Ontology`_ and KEGG_ websites.\n \n+.. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf\n+.. _Gene Ontology: http://www.geneontology.org\n+.. _KEGG: http://www.genome.jp/kegg\n \n- </help>\n+ ]]></help>\n <citations>\n <citation type="doi">10.1186/gb-2010-11-2-r14</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/dge_list_zf.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dge_list_zf.tab Mon Oct 23 11:19:12 2017 -0400 |
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| b'@@ -0,0 +1,632 @@\n+ENSDARG00000092696\tFALSE\n+ENSDARG00000104569\tTRUE\n+ENSDARG00000008472\tFALSE\n+ENSDARG00000058451\tFALSE\n+ENSDARG00000035957\tTRUE\n+ENSDARG00000043514\tFALSE\n+ENSDARG00000058114\tTRUE\n+ENSDARG00000102885\tFALSE\n+ENSDARG00000005451\tFALSE\n+ENSDARG00000058839\tFALSE\n+ENSDARG00000073999\tFALSE\n+ENSDARG00000079611\tFALSE\n+ENSDARG00000042623\tFALSE\n+ENSDARG00000044136\tFALSE\n+ENSDARG00000060983\tFALSE\n+ENSDARG00000108060\tFALSE\n+ENSDARG00000036852\tFALSE\n+ENSDARG00000089303\tFALSE\n+ENSDARG00000090013\tTRUE\n+ENSDARG00000042902\tFALSE\n+ENSDARG00000075203\tFALSE\n+ENSDARG00000069601\tTRUE\n+ENSDARG00000003822\tFALSE\n+ENSDARG00000057100\tFALSE\n+ENSDARG00000088508\tTRUE\n+ENSDARG00000026454\tTRUE\n+ENSDARG00000006399\tTRUE\n+ENSDARG00000079457\tTRUE\n+ENSDARG00000090654\tFALSE\n+ENSDARG00000092483\tFALSE\n+ENSDARG00000060627\tFALSE\n+ENSDARG00000039626\tFALSE\n+ENSDARG00000088475\tFALSE\n+ENSDARG00000055548\tFALSE\n+ENSDARG00000006196\tFALSE\n+ENSDARG00000035559\tFALSE\n+ENSDARG00000015254\tFALSE\n+ENSDARG00000031203\tFALSE\n+ENSDARG00000012790\tTRUE\n+ENSDARG00000004017\tTRUE\n+ENSDARG00000074558\tFALSE\n+ENSDARG00000043077\tTRUE\n+ENSDARG00000098550\tFALSE\n+ENSDARG00000095224\tFALSE\n+ENSDARG00000045352\tFALSE\n+ENSDARG00000079659\tFALSE\n+ENSDARG00000104567\tFALSE\n+ENSDARG00000060169\tFALSE\n+ENSDARG00000104837\tFALSE\n+ENSDARG00000097827\tFALSE\n+ENSDARG00000012684\tTRUE\n+ENSDARG00000002912\tFALSE\n+ENSDARG00000104861\tFALSE\n+ENSDARG00000089292\tFALSE\n+ENSDARG00000054903\tFALSE\n+ENSDARG00000031681\tFALSE\n+ENSDARG00000027586\tTRUE\n+ENSDARG00000061216\tFALSE\n+ENSDARG00000051853\tFALSE\n+ENSDARG00000062192\tFALSE\n+ENSDARG00000076568\tFALSE\n+ENSDARG00000004774\tFALSE\n+ENSDARG00000033889\tFALSE\n+ENSDARG00000044092\tFALSE\n+ENSDARG00000010098\tFALSE\n+ENSDARG00000043635\tTRUE\n+ENSDARG00000076804\tFALSE\n+ENSDARG00000061363\tFALSE\n+ENSDARG00000039522\tFALSE\n+ENSDARG00000022218\tFALSE\n+ENSDARG00000040024\tFALSE\n+ENSDARG00000019897\tFALSE\n+ENSDARG00000058701\tFALSE\n+ENSDARG00000036875\tTRUE\n+ENSDARG00000103380\tFALSE\n+ENSDARG00000025391\tFALSE\n+ENSDARG00000101637\tTRUE\n+ENSDARG00000067656\tTRUE\n+ENSDARG00000089467\tFALSE\n+ENSDARG00000002494\tFALSE\n+ENSDARG00000102896\tFALSE\n+ENSDARG00000100279\tFALSE\n+ENSDARG00000095969\tTRUE\n+ENSDARG00000039130\tTRUE\n+ENSDARG00000077060\tTRUE\n+ENSDARG00000037815\tFALSE\n+ENSDARG00000074170\tFALSE\n+ENSDARG00000013063\tTRUE\n+ENSDARG00000035570\tTRUE\n+ENSDARG00000104710\tFALSE\n+ENSDARG00000070168\tFALSE\n+ENSDARG00000052728\tTRUE\n+ENSDARG00000025949\tFALSE\n+ENSDARG00000076379\tFALSE\n+ENSDARG00000032631\tFALSE\n+ENSDARG00000024324\tFALSE\n+ENSDARG00000010445\tFALSE\n+ENSDARG00000008235\tTRUE\n+ENSDARG00000044752\tFALSE\n+ENSDARG00000099996\tFALSE\n+ENSDARG00000067719\tFALSE\n+ENSDARG00000063437\tFALSE\n+ENSDARG00000088631\tTRUE\n+ENSDARG00000074849\tFALSE\n+ENSDARG00000041853\tTRUE\n+ENSDARG00000060002\tTRUE\n+ENSDARG00000042977\tTRUE\n+ENSDARG00000043105\tFALSE\n+ENSDARG00000013842\tFALSE\n+ENSDARG00000004870\tTRUE\n+ENSDARG00000019000\tFALSE\n+ENSDARG00000100710\tTRUE\n+ENSDARG00000077988\tFALSE\n+ENSDARG00000073985\tFALSE\n+ENSDARG00000028192\tFALSE\n+ENSDARG00000075881\tFALSE\n+ENSDARG00000100203\tFALSE\n+ENSDARG00000073933\tFALSE\n+ENSDARG00000070478\tFALSE\n+ENSDARG00000068415\tFALSE\n+ENSDARG00000032765\tTRUE\n+ENSDARG00000092550\tTRUE\n+ENSDARG00000015678\tFALSE\n+ENSDARG00000075463\tFALSE\n+ENSDARG00000075172\tTRUE\n+ENSDARG00000098883\tFALSE\n+ENSDARG00000075721\tFALSE\n+ENSDARG00000017058\tFALSE\n+ENSDARG00000096249\tFALSE\n+ENSDARG00000059234\tTRUE\n+ENSDARG00000070644\tFALSE\n+ENSDARG00000035630\tFALSE\n+ENSDARG00000029003\tFALSE\n+ENSDARG00000073737\tFALSE\n+ENSDARG00000094336\tFALSE\n+ENSDARG00000058679\tFALSE\n+ENSDARG00000069266\tFALSE\n+ENSDARG00000002571\tFALSE\n+ENSDARG00000103594\tTRUE\n+ENSDARG00000041314\tFALSE\n+ENSDARG00000044490\tFALSE\n+ENSDARG00000075870\tFALSE\n+ENSDARG00000062646\tFALSE\n+ENSDARG00000053517\tTRUE\n+ENSDARG00000043334\tFALSE\n+ENSDARG00000076667\tFALSE\n+ENSDARG00000063375\tTRUE\n+ENSDARG00000104696\tFALSE\n+ENSDARG00000039125\tFALSE\n+ENSDARG00000078546\tFALSE\n+ENSDARG00000071060\tTRUE\n+ENSDARG00000077011\tTRUE\n+ENSDARG00000009953\tFALSE\n+ENSDARG00000038868\tFALSE\n+ENSDARG000001036'..b'17\tFALSE\n+ENSDARG00000070426\tTRUE\n+ENSDARG00000076110\tTRUE\n+ENSDARG00000090002\tFALSE\n+ENSDARG00000023111\tFALSE\n+ENSDARG00000012125\tFALSE\n+ENSDARG00000007172\tFALSE\n+ENSDARG00000026178\tFALSE\n+ENSDARG00000060445\tFALSE\n+ENSDARG00000018162\tTRUE\n+ENSDARG00000060661\tFALSE\n+ENSDARG00000013659\tFALSE\n+ENSDARG00000102744\tFALSE\n+ENSDARG00000071501\tFALSE\n+ENSDARG00000036090\tFALSE\n+ENSDARG00000045704\tFALSE\n+ENSDARG00000007221\tTRUE\n+ENSDARG00000041407\tFALSE\n+ENSDARG00000005356\tFALSE\n+ENSDARG00000102356\tTRUE\n+ENSDARG00000078479\tTRUE\n+ENSDARG00000029368\tTRUE\n+ENSDARG00000058992\tFALSE\n+ENSDARG00000027529\tFALSE\n+ENSDARG00000075369\tTRUE\n+ENSDARG00000063731\tTRUE\n+ENSDARG00000036542\tTRUE\n+ENSDARG00000014569\tTRUE\n+ENSDARG00000099298\tFALSE\n+ENSDARG00000091851\tFALSE\n+ENSDARG00000070698\tFALSE\n+ENSDARG00000088807\tFALSE\n+ENSDARG00000028725\tFALSE\n+ENSDARG00000039719\tFALSE\n+ENSDARG00000013732\tFALSE\n+ENSDARG00000037425\tTRUE\n+ENSDARG00000057151\tFALSE\n+ENSDARG00000092488\tFALSE\n+ENSDARG00000096454\tFALSE\n+ENSDARG00000070028\tFALSE\n+ENSDARG00000016710\tFALSE\n+ENSDARG00000075072\tFALSE\n+ENSDARG00000070867\tTRUE\n+ENSDARG00000037846\tFALSE\n+ENSDARG00000018600\tFALSE\n+ENSDARG00000013711\tFALSE\n+ENSDARG00000077081\tFALSE\n+ENSDARG00000067784\tFALSE\n+ENSDARG00000038731\tTRUE\n+ENSDARG00000035181\tFALSE\n+ENSDARG00000011240\tFALSE\n+ENSDARG00000075616\tTRUE\n+ENSDARG00000038442\tTRUE\n+ENSDARG00000002026\tTRUE\n+ENSDARG00000098618\tFALSE\n+ENSDARG00000069505\tFALSE\n+ENSDARG00000074892\tFALSE\n+ENSDARG00000055360\tFALSE\n+ENSDARG00000056797\tFALSE\n+ENSDARG00000017115\tFALSE\n+ENSDARG00000075533\tFALSE\n+ENSDARG00000091906\tFALSE\n+ENSDARG00000076501\tTRUE\n+ENSDARG00000017659\tTRUE\n+ENSDARG00000029660\tFALSE\n+ENSDARG00000004297\tFALSE\n+ENSDARG00000010280\tFALSE\n+ENSDARG00000022968\tFALSE\n+ENSDARG00000019033\tTRUE\n+ENSDARG00000015638\tFALSE\n+ENSDARG00000086550\tFALSE\n+ENSDARG00000007918\tFALSE\n+ENSDARG00000039677\tTRUE\n+ENSDARG00000073784\tTRUE\n+ENSDARG00000100862\tFALSE\n+ENSDARG00000003058\tFALSE\n+ENSDARG00000074644\tTRUE\n+ENSDARG00000013892\tFALSE\n+ENSDARG00000104348\tFALSE\n+ENSDARG00000053457\tTRUE\n+ENSDARG00000058351\tFALSE\n+ENSDARG00000034670\tTRUE\n+ENSDARG00000075169\tFALSE\n+ENSDARG00000078894\tFALSE\n+ENSDARG00000044090\tFALSE\n+ENSDARG00000092077\tTRUE\n+ENSDARG00000030694\tTRUE\n+ENSDARG00000016886\tTRUE\n+ENSDARG00000043339\tFALSE\n+ENSDARG00000103225\tFALSE\n+ENSDARG00000086411\tTRUE\n+ENSDARG00000104874\tFALSE\n+ENSDARG00000052747\tFALSE\n+ENSDARG00000075823\tTRUE\n+ENSDARG00000043843\tFALSE\n+ENSDARG00000077614\tTRUE\n+ENSDARG00000054220\tFALSE\n+ENSDARG00000009626\tFALSE\n+ENSDARG00000009023\tTRUE\n+ENSDARG00000045561\tFALSE\n+ENSDARG00000056559\tFALSE\n+ENSDARG00000017272\tTRUE\n+ENSDARG00000022788\tFALSE\n+ENSDARG00000018272\tFALSE\n+ENSDARG00000056473\tFALSE\n+ENSDARG00000099766\tTRUE\n+ENSDARG00000002991\tFALSE\n+ENSDARG00000104431\tFALSE\n+ENSDARG00000062465\tFALSE\n+ENSDARG00000054583\tTRUE\n+ENSDARG00000013802\tFALSE\n+ENSDARG00000057910\tTRUE\n+ENSDARG00000027984\tFALSE\n+ENSDARG00000045420\tFALSE\n+ENSDARG00000031359\tFALSE\n+ENSDARG00000056764\tFALSE\n+ENSDARG00000095594\tFALSE\n+ENSDARG00000076191\tFALSE\n+ENSDARG00000103251\tFALSE\n+ENSDARG00000039501\tTRUE\n+ENSDARG00000103589\tFALSE\n+ENSDARG00000051926\tFALSE\n+ENSDARG00000018681\tFALSE\n+ENSDARG00000014138\tTRUE\n+ENSDARG00000061462\tTRUE\n+ENSDARG00000102111\tFALSE\n+ENSDARG00000035819\tFALSE\n+ENSDARG00000076486\tFALSE\n+ENSDARG00000101799\tFALSE\n+ENSDARG00000008105\tFALSE\n+ENSDARG00000040387\tFALSE\n+ENSDARG00000060518\tFALSE\n+ENSDARG00000001244\tFALSE\n+ENSDARG00000005540\tFALSE\n+ENSDARG00000070055\tFALSE\n+ENSDARG00000073841\tFALSE\n+ENSDARG00000032117\tFALSE\n+ENSDARG00000087110\tFALSE\n+ENSDARG00000075641\tTRUE\n+ENSDARG00000001829\tFALSE\n+ENSDARG00000103786\tTRUE\n+ENSDARG00000058486\tFALSE\n+ENSDARG00000042272\tFALSE\n+ENSDARG00000000474\tFALSE\n+ENSDARG00000061635\tFALSE\n+ENSDARG00000095745\tFALSE\n+ENSDARG00000073801\tFALSE\n+ENSDARG00000028086\tFALSE\n+ENSDARG00000056583\tFALSE\n+ENSDARG00000033182\tTRUE\n+ENSDARG00000052703\tFALSE\n+ENSDARG00000051873\tFALSE\n+ENSDARG00000002267\tFALSE\n+ENSDARG00000091538\tFALSE\n+ENSDARG00000067713\tFALSE\n\\ No newline at end of file\n' |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/gc.tab --- a/test-data/gc.tab Sun Jun 11 08:57:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -ENSG00000162526 0.388349514563107 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/gene_length_zf.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_length_zf.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| b'@@ -0,0 +1,632 @@\n+ENSDARG00000092696\t6983\n+ENSDARG00000104569\t7302\n+ENSDARG00000008472\t1848\n+ENSDARG00000058451\t5878\n+ENSDARG00000035957\t3057\n+ENSDARG00000043514\t6176\n+ENSDARG00000058114\t5901\n+ENSDARG00000102885\t7262\n+ENSDARG00000005451\t9161\n+ENSDARG00000058839\t3602\n+ENSDARG00000073999\t2558\n+ENSDARG00000079611\t7620\n+ENSDARG00000042623\t2387\n+ENSDARG00000044136\t7553\n+ENSDARG00000060983\t8413\n+ENSDARG00000108060\t1774\n+ENSDARG00000036852\t3185\n+ENSDARG00000089303\t6313\n+ENSDARG00000090013\t3748\n+ENSDARG00000042902\t2536\n+ENSDARG00000075203\t2844\n+ENSDARG00000069601\t2545\n+ENSDARG00000003822\t2571\n+ENSDARG00000057100\t9297\n+ENSDARG00000088508\t5775\n+ENSDARG00000026454\t4448\n+ENSDARG00000006399\t9992\n+ENSDARG00000079457\t4005\n+ENSDARG00000090654\t2211\n+ENSDARG00000092483\t4033\n+ENSDARG00000060627\t10580\n+ENSDARG00000039626\t8419\n+ENSDARG00000088475\t7743\n+ENSDARG00000055548\t5115\n+ENSDARG00000006196\t3835\n+ENSDARG00000035559\t3281\n+ENSDARG00000015254\t8601\n+ENSDARG00000031203\t9908\n+ENSDARG00000012790\t14778\n+ENSDARG00000004017\t8583\n+ENSDARG00000074558\t3683\n+ENSDARG00000043077\t13733\n+ENSDARG00000098550\t4556\n+ENSDARG00000095224\t5969\n+ENSDARG00000045352\t4803\n+ENSDARG00000079659\t9493\n+ENSDARG00000104567\t5098\n+ENSDARG00000060169\t8487\n+ENSDARG00000104837\t15706\n+ENSDARG00000097827\t8517\n+ENSDARG00000012684\t5525\n+ENSDARG00000002912\t14371\n+ENSDARG00000104861\t12106\n+ENSDARG00000089292\t11052\n+ENSDARG00000054903\t1097\n+ENSDARG00000031681\t9198\n+ENSDARG00000027586\t3839\n+ENSDARG00000061216\t9084\n+ENSDARG00000051853\t3428\n+ENSDARG00000062192\t13781\n+ENSDARG00000076568\t6265\n+ENSDARG00000004774\t5463\n+ENSDARG00000033889\t3833\n+ENSDARG00000044092\t5870\n+ENSDARG00000010098\t13674\n+ENSDARG00000043635\t9947\n+ENSDARG00000076804\t5325\n+ENSDARG00000061363\t7039\n+ENSDARG00000039522\t4253\n+ENSDARG00000022218\t6814\n+ENSDARG00000040024\t4194\n+ENSDARG00000019897\t3572\n+ENSDARG00000058701\t5106\n+ENSDARG00000036875\t3762\n+ENSDARG00000103380\t9352\n+ENSDARG00000025391\t3212\n+ENSDARG00000101637\t3824\n+ENSDARG00000067656\t2864\n+ENSDARG00000089467\t2928\n+ENSDARG00000002494\t9067\n+ENSDARG00000102896\t4563\n+ENSDARG00000100279\t4447\n+ENSDARG00000095969\t5974\n+ENSDARG00000039130\t2856\n+ENSDARG00000077060\t6138\n+ENSDARG00000037815\t5299\n+ENSDARG00000074170\t5991\n+ENSDARG00000013063\t4982\n+ENSDARG00000035570\t2532\n+ENSDARG00000104710\t10945\n+ENSDARG00000070168\t12705\n+ENSDARG00000052728\t4646\n+ENSDARG00000025949\t7324\n+ENSDARG00000076379\t4713\n+ENSDARG00000032631\t6641\n+ENSDARG00000024324\t12238\n+ENSDARG00000010445\t2030\n+ENSDARG00000008235\t2405\n+ENSDARG00000044752\t4377\n+ENSDARG00000099996\t19998\n+ENSDARG00000067719\t8015\n+ENSDARG00000063437\t7223\n+ENSDARG00000088631\t1836\n+ENSDARG00000074849\t8477\n+ENSDARG00000041853\t10888\n+ENSDARG00000060002\t7217\n+ENSDARG00000042977\t10000\n+ENSDARG00000043105\t4213\n+ENSDARG00000013842\t4742\n+ENSDARG00000004870\t9022\n+ENSDARG00000019000\t11768\n+ENSDARG00000100710\t8586\n+ENSDARG00000077988\t5539\n+ENSDARG00000073985\t2740\n+ENSDARG00000028192\t12781\n+ENSDARG00000075881\t7046\n+ENSDARG00000100203\t3507\n+ENSDARG00000073933\t7594\n+ENSDARG00000070478\t6618\n+ENSDARG00000068415\t5055\n+ENSDARG00000032765\t2550\n+ENSDARG00000092550\t9112\n+ENSDARG00000015678\t5184\n+ENSDARG00000075463\t5802\n+ENSDARG00000075172\t2813\n+ENSDARG00000098883\t2251\n+ENSDARG00000075721\t4428\n+ENSDARG00000017058\t7437\n+ENSDARG00000096249\t5481\n+ENSDARG00000059234\t9240\n+ENSDARG00000070644\t1838\n+ENSDARG00000035630\t6902\n+ENSDARG00000029003\t9484\n+ENSDARG00000073737\t5717\n+ENSDARG00000094336\t1190\n+ENSDARG00000058679\t4183\n+ENSDARG00000069266\t10601\n+ENSDARG00000002571\t2682\n+ENSDARG00000103594\t928\n+ENSDARG00000041314\t4275\n+ENSDARG00000044490\t7345\n+ENSDARG00000075870\t11038\n+ENSDARG00000062646\t7411\n+ENSDARG00000053517\t5740\n+ENSDARG00000043334\t8151\n+ENSDARG00000076667\t3222\n+ENSDARG00000063375\t3847\n+ENSDARG00000104696\t3177\n+ENSDARG00000039125\t3889\n+ENSDARG00000078546\t6524\n+ENSDARG00000071060\t2128\n+ENSDARG00000077011\t3434\n+ENSDARG00000009953\t7360\n+ENSDARG00000038868\t6297\n+ENSDARG00000103610\t7596\n+ENSDARG00000041619\t5566\n+ENSDARG00000026109\t6403\n+ENSDARG00000003564\t4830\n+ENSDARG00000'..b'000090543\t6309\n+ENSDARG00000103902\t3149\n+ENSDARG00000060215\t11708\n+ENSDARG00000045909\t861\n+ENSDARG00000055917\t2191\n+ENSDARG00000070426\t5827\n+ENSDARG00000076110\t4980\n+ENSDARG00000090002\t1848\n+ENSDARG00000023111\t6716\n+ENSDARG00000012125\t3204\n+ENSDARG00000007172\t3265\n+ENSDARG00000026178\t680\n+ENSDARG00000060445\t6490\n+ENSDARG00000018162\t7777\n+ENSDARG00000060661\t3630\n+ENSDARG00000013659\t4736\n+ENSDARG00000102744\t3411\n+ENSDARG00000071501\t5593\n+ENSDARG00000036090\t6565\n+ENSDARG00000045704\t3313\n+ENSDARG00000007221\t10574\n+ENSDARG00000041407\t8668\n+ENSDARG00000005356\t11291\n+ENSDARG00000102356\t5023\n+ENSDARG00000078479\t2775\n+ENSDARG00000029368\t4290\n+ENSDARG00000058992\t8283\n+ENSDARG00000027529\t7190\n+ENSDARG00000075369\t5051\n+ENSDARG00000063731\t7422\n+ENSDARG00000036542\t2676\n+ENSDARG00000014569\t7375\n+ENSDARG00000099298\t5756\n+ENSDARG00000091851\t8467\n+ENSDARG00000070698\t3395\n+ENSDARG00000088807\t4319\n+ENSDARG00000028725\t4065\n+ENSDARG00000039719\t9199\n+ENSDARG00000013732\t1092\n+ENSDARG00000037425\t6768\n+ENSDARG00000057151\t15144\n+ENSDARG00000092488\t2085\n+ENSDARG00000096454\t6749\n+ENSDARG00000070028\t2866\n+ENSDARG00000016710\t1806\n+ENSDARG00000075072\t7179\n+ENSDARG00000070867\t11000\n+ENSDARG00000037846\t2326\n+ENSDARG00000018600\t15242\n+ENSDARG00000013711\t3301\n+ENSDARG00000077081\t3115\n+ENSDARG00000067784\t15701\n+ENSDARG00000038731\t4003\n+ENSDARG00000035181\t8260\n+ENSDARG00000011240\t4901\n+ENSDARG00000075616\t2423\n+ENSDARG00000038442\t7459\n+ENSDARG00000002026\t3070\n+ENSDARG00000098618\t6180\n+ENSDARG00000069505\t2082\n+ENSDARG00000074892\t12773\n+ENSDARG00000055360\t7068\n+ENSDARG00000056797\t5199\n+ENSDARG00000017115\t3193\n+ENSDARG00000075533\t7239\n+ENSDARG00000091906\t8184\n+ENSDARG00000076501\t2093\n+ENSDARG00000017659\t3157\n+ENSDARG00000029660\t4699\n+ENSDARG00000004297\t3420\n+ENSDARG00000010280\t2807\n+ENSDARG00000022968\t2165\n+ENSDARG00000019033\t7868\n+ENSDARG00000015638\t3285\n+ENSDARG00000086550\t3859\n+ENSDARG00000007918\t5611\n+ENSDARG00000039677\t2769\n+ENSDARG00000073784\t2745\n+ENSDARG00000100862\t6157\n+ENSDARG00000003058\t2889\n+ENSDARG00000074644\t6922\n+ENSDARG00000013892\t5034\n+ENSDARG00000104348\t3245\n+ENSDARG00000053457\t7776\n+ENSDARG00000058351\t4276\n+ENSDARG00000034670\t5499\n+ENSDARG00000075169\t1365\n+ENSDARG00000078894\t4153\n+ENSDARG00000044090\t7828\n+ENSDARG00000092077\t7775\n+ENSDARG00000030694\t2395\n+ENSDARG00000016886\t5872\n+ENSDARG00000043339\t8700\n+ENSDARG00000103225\t3074\n+ENSDARG00000086411\t2266\n+ENSDARG00000104874\t2861\n+ENSDARG00000052747\t8005\n+ENSDARG00000075823\t2917\n+ENSDARG00000043843\t3153\n+ENSDARG00000077614\t4371\n+ENSDARG00000054220\t8511\n+ENSDARG00000009626\t8938\n+ENSDARG00000009023\t3406\n+ENSDARG00000045561\t3929\n+ENSDARG00000056559\t8333\n+ENSDARG00000017272\t7464\n+ENSDARG00000022788\t3285\n+ENSDARG00000018272\t1753\n+ENSDARG00000056473\t594\n+ENSDARG00000099766\t3391\n+ENSDARG00000002991\t3520\n+ENSDARG00000104431\t3327\n+ENSDARG00000062465\t497\n+ENSDARG00000054583\t3030\n+ENSDARG00000013802\t2392\n+ENSDARG00000057910\t3804\n+ENSDARG00000027984\t4204\n+ENSDARG00000045420\t4427\n+ENSDARG00000031359\t8630\n+ENSDARG00000056764\t3765\n+ENSDARG00000095594\t4175\n+ENSDARG00000076191\t4849\n+ENSDARG00000103251\t10864\n+ENSDARG00000039501\t6145\n+ENSDARG00000103589\t7977\n+ENSDARG00000051926\t8640\n+ENSDARG00000018681\t5479\n+ENSDARG00000014138\t6138\n+ENSDARG00000061462\t15787\n+ENSDARG00000102111\t9423\n+ENSDARG00000035819\t1981\n+ENSDARG00000076486\t7968\n+ENSDARG00000101799\t3670\n+ENSDARG00000008105\t8787\n+ENSDARG00000040387\t4616\n+ENSDARG00000060518\t8331\n+ENSDARG00000001244\t1781\n+ENSDARG00000005540\t1155\n+ENSDARG00000070055\t5411\n+ENSDARG00000073841\t4224\n+ENSDARG00000032117\t3659\n+ENSDARG00000087110\t5459\n+ENSDARG00000075641\t2527\n+ENSDARG00000001829\t2989\n+ENSDARG00000103786\t15155\n+ENSDARG00000058486\t5559\n+ENSDARG00000042272\t6005\n+ENSDARG00000000474\t2047\n+ENSDARG00000061635\t5731\n+ENSDARG00000095745\t2551\n+ENSDARG00000073801\t6118\n+ENSDARG00000028086\t8075\n+ENSDARG00000056583\t9656\n+ENSDARG00000033182\t2331\n+ENSDARG00000052703\t6689\n+ENSDARG00000051873\t4234\n+ENSDARG00000002267\t8114\n+ENSDARG00000091538\t8260\n+ENSDARG00000067713\t853\n\\ No newline at end of file\n' |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/getgo.danRer10.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getgo.danRer10.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p.adjust.over_represented p.adjust.under_represented +GO:0031324 0.019289727841568 0.997004018824821 6 9 negative regulation of cellular metabolic process BP 1 1 +GO:0040011 0.0219399815699082 0.993554925323586 10 19 locomotion BP 1 1 +GO:0048738 0.0232122438335162 1 3 3 cardiac muscle tissue development BP 1 1 +GO:0031101 0.0232122438335199 1 3 3 fin regeneration BP 1 1 +GO:0042246 0.0232122438335199 1 3 3 tissue regeneration BP 1 1 +GO:0007050 0.023212243833521 1 3 3 cell cycle arrest BP 1 1 +GO:0019783 0.0254384360641003 0.998148600664743 4 5 ubiquitin-like protein-specific protease activity MF 1 1 +GO:0036459 0.0254384360641003 0.998148600664743 4 5 thiol-dependent ubiquitinyl hydrolase activity MF 1 1 +GO:0101005 0.0254384360641003 0.998148600664743 4 5 ubiquitinyl hydrolase activity MF 1 1 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/getgo.hg38.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/getgo.hg38.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| @@ -0,0 +1,10 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p.adjust.over_represented p.adjust.under_represented +GO:0005576 4.72734295222294e-05 0.999979271555286 56 142 extracellular region CC 0.329456825863645 1 +GO:0005840 0.000150633625443482 0.999987765310632 9 12 ribosome CC 0.329456825863645 1 +GO:0044763 0.000210237360853053 0.999883100939053 148 473 single-organism cellular process BP 0.329456825863645 1 +GO:0044699 0.000229197548055812 0.999873090122854 158 513 single-organism process BP 0.329456825863645 1 +GO:0065010 0.000394294879818402 0.999824474827037 43 108 extracellular membrane-bounded organelle CC 0.329456825863645 1 +GO:0070062 0.000394294879818402 0.999824474827037 43 108 extracellular exosome CC 0.329456825863645 1 +GO:0008150 0.000409074003076654 0.999785179807024 191 656 biological_process BP 0.329456825863645 1 +GO:0005488 0.000447980265756431 0.99975072864471 175 589 binding MF 0.329456825863645 1 +GO:0005198 0.000511195682086445 0.999905085898726 13 21 structural molecule activity MF 0.329456825863645 1 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/go_terms.tab --- a/test-data/go_terms.tab Sun Jun 11 08:57:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,85 +0,0 @@ -ENSG00000162526 GO:0000003 -ENSG00000162526 GO:0000166 -ENSG00000162526 GO:0000287 -ENSG00000162526 GO:0001882 -ENSG00000162526 GO:0001883 -ENSG00000162526 GO:0003674 -ENSG00000162526 GO:0003824 -ENSG00000162526 GO:0004672 -ENSG00000162526 GO:0004674 -ENSG00000162526 GO:0005488 -ENSG00000162526 GO:0005515 -ENSG00000162526 GO:0005524 -ENSG00000162526 GO:0005575 -ENSG00000162526 GO:0005622 -ENSG00000162526 GO:0005623 -ENSG00000162526 GO:0005737 -ENSG00000162526 GO:0006464 -ENSG00000162526 GO:0006468 -ENSG00000162526 GO:0006793 -ENSG00000162526 GO:0006796 -ENSG00000162526 GO:0007154 -ENSG00000162526 GO:0007165 -ENSG00000162526 GO:0007275 -ENSG00000162526 GO:0007276 -ENSG00000162526 GO:0007283 -ENSG00000162526 GO:0008150 -ENSG00000162526 GO:0008152 -ENSG00000162526 GO:0009987 -ENSG00000162526 GO:0016301 -ENSG00000162526 GO:0016310 -ENSG00000162526 GO:0016740 -ENSG00000162526 GO:0016772 -ENSG00000162526 GO:0016773 -ENSG00000162526 GO:0017076 -ENSG00000162526 GO:0019538 -ENSG00000162526 GO:0019953 -ENSG00000162526 GO:0022414 -ENSG00000162526 GO:0023052 -ENSG00000162526 GO:0030154 -ENSG00000162526 GO:0030554 -ENSG00000162526 GO:0032501 -ENSG00000162526 GO:0032502 -ENSG00000162526 GO:0032504 -ENSG00000162526 GO:0032549 -ENSG00000162526 GO:0032550 -ENSG00000162526 GO:0032553 -ENSG00000162526 GO:0032555 -ENSG00000162526 GO:0032559 -ENSG00000162526 GO:0035556 -ENSG00000162526 GO:0035639 -ENSG00000162526 GO:0036094 -ENSG00000162526 GO:0036211 -ENSG00000162526 GO:0043167 -ENSG00000162526 GO:0043168 -ENSG00000162526 GO:0043169 -ENSG00000162526 GO:0043170 -ENSG00000162526 GO:0043412 -ENSG00000162526 GO:0044237 -ENSG00000162526 GO:0044238 -ENSG00000162526 GO:0044260 -ENSG00000162526 GO:0044267 -ENSG00000162526 GO:0044424 -ENSG00000162526 GO:0044464 -ENSG00000162526 GO:0044699 -ENSG00000162526 GO:0044700 -ENSG00000162526 GO:0044702 -ENSG00000162526 GO:0044703 -ENSG00000162526 GO:0044707 -ENSG00000162526 GO:0044763 -ENSG00000162526 GO:0044767 -ENSG00000162526 GO:0046872 -ENSG00000162526 GO:0048232 -ENSG00000162526 GO:0048609 -ENSG00000162526 GO:0048869 -ENSG00000162526 GO:0050789 -ENSG00000162526 GO:0050794 -ENSG00000162526 GO:0050896 -ENSG00000162526 GO:0051704 -ENSG00000162526 GO:0051716 -ENSG00000162526 GO:0065007 -ENSG00000162526 GO:0071704 -ENSG00000162526 GO:0097159 -ENSG00000162526 GO:0097367 -ENSG00000162526 GO:1901265 -ENSG00000162526 GO:1901363 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/goseq_analysis.RData |
| b |
| Binary file test-data/goseq_analysis.RData has changed |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/length.tab --- a/test-data/length.tab Sun Jun 11 08:57:39 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -ENSG00000162526 103 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/length_bias_plot.pdf |
| b |
| Binary file test-data/length_bias_plot.pdf has changed |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/nobias.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nobias.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p.adjust.over_represented p.adjust.under_represented +GO:0000278 0.0129827306163772 0.999244816412166 4 5 mitotic cell cycle BP 0.0259654612327543 0.999244816412166 +GO:0000003 1 0.761 0 1 reproduction BP 1 0.999244816412166 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/samp.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samp.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p.adjust.over_represented p.adjust.under_represented +GO:0000278 0.016983016983017 1 4 5 mitotic cell cycle BP 0.033966033966034 1 +GO:0000003 1 0.802197802197802 0 1 reproduction BP 1 1 |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/sample_vs_wallenius_plot.pdf |
| b |
| Binary file test-data/sample_vs_wallenius_plot.pdf has changed |
| b |
| diff -r 9d1256d9ef0b -r ab492df30cdf test-data/wal.tab --- a/test-data/wal.tab Sun Jun 11 08:57:39 2017 -0400 +++ b/test-data/wal.tab Mon Oct 23 11:19:12 2017 -0400 |
| b |
| @@ -1,3 +1,3 @@ -category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p\.adjust.over_represented p\.adjust.under_represented -GO:0000278 0\.0122.+ 0\.999.+ 4 5 mitotic cell cycle BP 0\.0245.+ 0\.999.+ -GO:0000003 1 0\.796.+ 0 1 reproduction BP 1 0\.999.+ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology p.adjust.over_represented p.adjust.under_represented +GO:0000278 0.0112350612534339 0.999376653834006 4 5 mitotic cell cycle BP 0.0224701225068678 0.999376653834006 +GO:0000003 1 0.805913166914892 0 1 reproduction BP 1 0.999376653834006 |