Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate goseq.r @ 5:b79c65c90744 draft

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author mvdbeek
date Sun, 28 Feb 2016 11:52:10 -0500
parents 76eab486aba9
children 0e9424413ab0
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mvdbeek
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1 sink(stdout(), type = "message")
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mvdbeek
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2 suppressWarnings(suppressMessages(library(goseq)))
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mvdbeek
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3 suppressWarnings(suppressMessages(library(optparse)))
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mvdbeek
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5 option_list <- list(
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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6 make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"),
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7 make_option(c("-w","--wallenius_tab"), type="character", help="Path to output file with P-values estimated using wallenius distribution."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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8 make_option(c("-s","--sampling_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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9 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."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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10 make_option(c("-l","--length_bias_plot"), type="character", default=FALSE, help="Path to length-bias plot."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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11 make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."),
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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12 make_option(c("-padj", "--p_adj_column"), type="integer",help="Column that contains p. adjust values"),
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13 make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff",
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14 help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"),
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15 make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"),
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16 make_option(c("-lf", "--length_file"), type="character", default="FALSE", help = "Path to tabular file mapping gene id to length"),
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17 make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"),
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18 make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file"),
b79c65c90744 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit 81aedf1b50849160f6c048c0da4bb1038bb813a5
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19 make_option(c("-cat", "--use_genes_without_cat"), default=FALSE, type="logical", help="A boolean to indicate whether genes without a categorie should still be used. For example, a large number of gene may have no GO term annotated. If thisoption is set to FALSE, those genes will be ignored in the calculation of p-values(default behaviour). If this option is set to TRUE, then these genes will count towards the total number of genes outside the category being tested (default behaviour prior to version 1.15.2)."
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mvdbeek
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20 )
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21 )
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22 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
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23 args = parse_args(parser)
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25 # Vars:
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26 dge_file = args$dge_file
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27 p_adj_column = args$p_adj_colum
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28 p_adj_cutoff = args$p_adj_cutoff
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29 length_file = args$length_file
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30 genome = args$genome
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31 gene_id = args$gene_id
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32 wallenius_tab = args$wallenius_tab
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33 sampling_tab = args$sampling_tab
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34 nobias_tab = args$nobias_tab
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35 length_bias_plot = args$length_bias_plot
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36 sample_vs_wallenius_plot = args$sample_vs_wallenius_plot
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37 repcnt = args$repcnt
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38 use_genes_without_cat = args$use_genes_without_cat
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39
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40 # format DE genes into vector suitable for use with goseq
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41 dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE)
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42 genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
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43 names(genes) = dge_table[,1] # Assuming first row contains gene names
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45 # Get gene lengths
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46 if (length_file != "FALSE" ) {
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47 length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE)
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48 row.names(length_table) = length_table[,1]
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49 gene_lengths = length_table[names(genes),]$length
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50 } else {
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51 gene_lengths = getlength(names(genes), genome, gene_id)
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52 }
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54 # Estimate PWF
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56 pdf(length_bias_plot)
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57 pwf=nullp(genes, genome, gene_id, gene_lengths)
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58 message = dev.off()
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60 # Fetch GO annotations:
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61 go_map=getgo(names(genes), genome, gene_id, fetch.cats=c("GO:CC", "GO:BP", "GO:MF", "KEGG"))
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62
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63 # wallenius approximation of p-values
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64 GO.wall=goseq(pwf, genome, gene_id, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
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65
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66 GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric", use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
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68 # Sampling distribution
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69 if (repcnt > 0) {
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70 GO.samp=goseq(pwf,genome, gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
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71 # Compare sampling with wallenius
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72 pdf(sample_vs_wallenius_plot)
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73 plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]),
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74 xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)",
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75 xlim=c(-3,0))
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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76 abline(0,1,col=3,lty=2)
3
81283f3d65c7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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77 message = dev.off()
0
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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78 write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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79 }
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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80
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81
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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82 write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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83 write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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84
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mvdbeek
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85 sessionInfo()
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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86
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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87 # Use the following to get a list of supported genomes / gene ids
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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88
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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89 # write.table(supportedGenomes(), "available_genomes.tab", row.names = FALSE, quote=FALSE)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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90 # write.table(supportedGeneIDs(), "supported_gene_ids.tab", row.name = FALSE, quote = FALSE)
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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91 # write.table(table.summary, "input_gene_count_matrix.tab", row.names = FALSE, quote = FALSE)