Mercurial > repos > mvdbeek > r_goseq_1_22_0

annotate goseq.r @ 2:0283381bdafd draft

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author mvdbeek
date Fri, 26 Feb 2016 08:49:05 -0500
parents a6427f7893b0
children 81283f3d65c7
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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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1 sink(stdout(), type = "message")
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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2 library(goseq)
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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3 library(optparse)
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mvdbeek
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4
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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"),
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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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
mvdbeek
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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"),
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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13 make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff",
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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14 help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"),
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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15 make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"),
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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16 make_option(c("-lf", "--length_file"), default=FALSE, help = "Path to "),
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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17 make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"),
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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18 make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file")
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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19 )
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20 parser <- OptionParser(usage = "%prog [options] file", option_list=option_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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21 args = parse_args(parser)
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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22
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23 # Vars:
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24 dge_file = args$dge_file
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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25 p_adj_column = args$p_adj_colum
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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26 p_adj_cutoff = args$p_adj_cutoff
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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27 length_file = args$length_file
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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28 genome = args$genome
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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29 gene_id = args$gene_id
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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30 wallenius_tab = args$wallenius_tab
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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31 sampling_tab = args$sampling_tab
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32 nobias_tab = args$nobias_tab
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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33 length_bias_plot = args$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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34 sample_vs_wallenius_plot = args$sample_vs_wallenius_plot
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
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35 repcnt = args$repcnt
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36
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37
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38 # format DE genes into vector suitable for use with goseq
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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39 dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = 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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40 genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
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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41 names(genes) = dge_table[,1] # Assuming first row contains gene names
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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42
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43 # Get gene lengths
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44
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45 if (length_file) {
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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46 length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE)
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47 gene_lengths = length_table[names(genes),]$length
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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48 } else {
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49 gene_lengths = getlength(names(genes), genome, gene_id)
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50 }
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51
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52 # Estimate PWF
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53
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54 pdf(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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55 pwf=nullp(genes, genome, gene_id, gene_lengths)
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56 dev.off()
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57 # wallenius approximation of p-values
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58 GO.wall=goseq(pwf, genome, gene_id)
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59
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60 GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric")
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61
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62 # Sampling distribution
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63 if (repcnt > 0) {
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64 GO.samp=goseq(pwf,genome, gene_id, method="Sampling", repcnt=repcnt)
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65 # Compare sampling with wallenius
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66 pdf(sample_vs_wallenius_plot)
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67 plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]),
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68 xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)",
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69 xlim=c(-3,0))
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70 abline(0,1,col=3,lty=2)
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71 dev.off()
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72 write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
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73 }
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74
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75
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76 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
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77 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
mvdbeek
parents:
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78
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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79 sessionInfo()
a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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81 # 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
mvdbeek
parents:
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a6427f7893b0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
parents:
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83 # 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
mvdbeek
parents:
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84 # 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
mvdbeek
parents:
diff changeset
85 # write.table(table.summary, "input_gene_count_matrix.tab", row.names = FALSE, quote = FALSE)