Mercurial > repos > artbio > gsc_filter_genes
annotate filter_genes.R @ 2:afe949d332b3 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
author | artbio |
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date | Mon, 16 Oct 2023 23:26:20 +0000 |
parents | 5d2304b09f58 |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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1 # Filter out low expressed genes |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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2 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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3 # Example of command (used for generate output file) : |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 # Rscript filter_genes.R -f <input file> -o <output file> |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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5 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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6 # load packages that are provided in the conda env |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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7 options(show.error.messages = FALSE, |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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8 error = function() { |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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9 cat(geterrmessage(), file = stderr()) |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
artbio
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10 q("no", 1, FALSE) |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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11 } |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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12 ) |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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13 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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14 library(optparse) |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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15 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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16 # Arguments |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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17 option_list <- list( |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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18 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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19 c("-f", "--input"), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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20 default = NA, |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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21 type = "character", |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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22 help = "Input file that contains count values to filter" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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23 ), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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24 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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25 c("-s", "--sep"), |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
artbio
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26 default = "\t", |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
artbio
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27 type = "character", |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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28 help = "File separator [default : '%default' ]" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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29 ), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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30 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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31 c("-c", "--colnames"), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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32 default = TRUE, |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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33 type = "logical", |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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34 help = "first line is a header [default : '%default' ]" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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35 ), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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36 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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37 "--percentile_detection", |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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38 default = 0, |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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39 type = "numeric", |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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40 help = "Include genes with detected expression in at least \ |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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41 this fraction of cells [default : '%default' ]" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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42 ), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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43 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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44 "--absolute_detection", |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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45 default = 0, |
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afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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46 type = "numeric", |
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f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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47 help = "Include genes with detected expression in at least \ |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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48 this number of cells [default : '%default' ]" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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49 ), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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50 make_option( |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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51 c("-o", "--output"), |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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52 default = NA, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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53 type = "character", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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54 help = "Output name [default : '%default' ]" |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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55 ) |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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56 ) |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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57 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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58 opt <- parse_args(OptionParser(option_list = option_list), |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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59 args = commandArgs(trailingOnly = TRUE)) |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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60 if (opt$sep == "tab") { |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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61 opt$sep <- "\t" |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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62 } |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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63 if (opt$sep == "comma") { |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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64 opt$sep <- "," |
afe949d332b3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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65 } |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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66 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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67 # Open files |
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68 data.counts <- read.delim( |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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69 opt$input, |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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70 h = opt$colnames, |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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71 row.names = 1, |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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72 sep = opt$sep, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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73 check.names = FALSE |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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74 ) |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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75 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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76 # note the [if else] below, to handle percentile_detection=absolute_detection=0 |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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77 # Search for genes that are expressed in a certain percent of cells |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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78 if (opt$percentile_detection > 0) { |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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79 kept_genes <- rowSums(data.counts != 0) >= (opt$percentile_detection * ncol(data.counts)) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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80 } else { |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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81 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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82 # Search for genes that are expressed in more than an absolute number of cells |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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83 kept_genes <- rowSums(data.counts != 0) >= (opt$absolute_detection) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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84 } |
f689c4ea8c43
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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85 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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86 # Filter matrix |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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87 data.counts <- data.counts[kept_genes, ] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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88 data.counts <- cbind(Genes = rownames(data.counts), data.counts) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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89 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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90 # Save filtered matrix |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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91 write.table( |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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92 data.counts, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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93 opt$output, |
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94 sep = "\t", |
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95 quote = FALSE, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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96 col.names = TRUE, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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97 row.names = FALSE |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes commit b184054ad6d4230ab0a714c13f9ef32449faa327
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98 ) |