Mercurial > repos > artbio > gsc_signature_score
annotate signature_score.R @ 0:baf7a079bce0 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
author | artbio |
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date | Mon, 24 Jun 2019 13:40:08 -0400 |
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children | e08419b8ec24 |
rev | line source |
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0
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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1 ######################### |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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2 # Signature score # |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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3 ######################### |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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5 # Compute the signature score based on the geometric mean of the target gene expression |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6 # and split cells in 2 groups (high/low) using this signature score. |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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8 # Example of command |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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9 # Rscript 4-signature_score.R --input <input.tsv> --genes ARNT2,SALL2,SOX9,OLIG2,POU3F2 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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10 # --output <output.tab> --pdf <output.pdf> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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12 # load packages that are provided in the conda env |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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13 options( show.error.messages=F, |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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14 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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16 warnings() |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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17 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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18 library(optparse) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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19 library(psych) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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20 library(ggplot2) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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21 library(gridExtra) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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22 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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23 # Arguments |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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24 option_list = list( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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25 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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26 "--input", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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27 default = NA, |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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28 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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29 help = "Input file that contains log2(CPM +1) values" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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30 ), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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31 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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32 "--sep", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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33 default = '\t', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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34 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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35 help = "File separator [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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36 ), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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37 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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38 "--colnames", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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39 default = TRUE, |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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40 type = 'logical', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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41 help = "Consider first line as header ? [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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42 ), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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43 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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44 "--genes", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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45 default = NA, |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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46 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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47 help = "List of genes comma separated" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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48 ), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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49 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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50 "--percentile_threshold", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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51 default = 20, |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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52 type = 'integer', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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53 help = "detection threshold to keep a gene in signature set [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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54 ), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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55 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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56 "--output", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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57 default = "./output.tab", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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58 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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59 help = "Output path [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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60 ), |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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61 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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62 "--stats", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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63 default = "./statistics.tab", |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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64 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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65 help = "statistics path [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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66 ), |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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67 make_option( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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68 "--pdf", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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69 default = "~/output.pdf", |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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70 type = 'character', |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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71 help = "pdf path [default : '%default' ]" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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72 ) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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73 ) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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74 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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75 opt = parse_args(OptionParser(option_list = option_list), |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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76 args = commandArgs(trailingOnly = TRUE)) |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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77 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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78 if (opt$sep == "tab") {opt$sep = "\t"} |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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79 if (opt$sep == "comma") {opt$sep = ","} |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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80 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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81 # Take input data |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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82 data.counts <- read.table( |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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83 opt$input, |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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84 h = opt$colnames, |
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85 row.names = 1, |
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86 sep = opt$sep, |
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87 check.names = F |
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88 ) |
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89 |
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90 # Get vector of target genes |
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91 genes <- unlist(strsplit(opt$genes, ",")) |
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92 |
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93 if (length(unique(genes %in% rownames(data.counts))) == 1) { |
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94 if (unique(genes %in% rownames(data.counts)) == F) |
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95 stop("None of these genes are in your dataset: ", opt$genes) |
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96 } |
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97 |
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98 logical_genes <- rownames(data.counts) %in% genes |
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99 |
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100 # Retrieve target genes in counts data |
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101 signature.counts <- subset(data.counts, logical_genes) |
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102 |
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103 |
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104 ## Descriptive Statistics Function |
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105 descriptive_stats = function(InputData) { |
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106 SummaryData = data.frame( |
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107 mean = rowMeans(InputData), |
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108 SD = apply(InputData, 1, sd), |
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109 Variance = apply(InputData, 1, var), |
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110 Percentage_Detection = apply(InputData, 1, function(x, y = InputData) { |
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111 (sum(x != 0) / ncol(y)) * 100 |
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112 }) |
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113 ) |
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114 return(SummaryData) |
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115 } |
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116 |
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117 signature_stats <- descriptive_stats(signature.counts) |
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118 |
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119 # Find poorly detected genes from the signature |
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120 kept_genes <- signature_stats$Percentage_Detection >= opt$percentile_threshold |
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121 |
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122 # Add warnings |
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123 if (length(unique(kept_genes)) > 1) { |
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124 cat( |
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125 "WARNINGS ! Following genes were removed from further analysis due to low gene expression :", |
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126 paste(paste(rownames(signature.counts)[!kept_genes], round(signature_stats$Percentage_Detection[!kept_genes], 2), sep = " : "), collapse = ", "), |
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127 "\n" |
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128 ) |
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129 } else { |
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130 if (unique(kept_genes) == F) { |
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131 stop( |
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132 "None of these genes are detected in ", |
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133 opt$percent, |
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134 "% of your cells: ", |
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135 paste(rownames(signature_stats), collapse = ", "), |
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136 ". You can be less stringent thanks to --percent parameter." |
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137 ) |
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138 } |
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139 } |
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140 |
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141 # Remove genes poorly detected in the dataset |
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142 signature.counts <- signature.counts[kept_genes,] |
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143 |
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144 # Replace 0 by 1 counts |
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145 signature.counts[signature.counts == 0] <- 1 |
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146 |
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147 # Geometric mean by cell |
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148 score <- apply(signature.counts, 2, geometric.mean) # geometric.mean requires psych |
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149 |
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150 # Add results in signature_output |
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151 signature_output <- data.frame( |
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152 cell = names(score), |
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153 score = score, |
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154 rate = ifelse(score > mean(score), "HIGH", "LOW"), |
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155 nGenes = colSums(data.counts != 0), |
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156 total_counts = colSums(data.counts) |
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157 ) |
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158 |
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159 # statistics of input genes, signature genes first lines |
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160 statistics.counts <- rbind(subset(data.counts, logical_genes), |
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161 subset(data.counts, !logical_genes)) |
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162 statistics <- descriptive_stats(statistics.counts) |
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163 statistics <- cbind(gene=rownames(statistics), statistics) |
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164 |
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165 |
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166 |
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167 # Re-arrange score matrix for plots |
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168 score <- data.frame(score = score, |
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169 order = rank(score, ties.method = "first"), |
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170 signature = signature_output$rate, |
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171 stringsAsFactors = F) |
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172 |
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173 pdf(file = opt$pdf) |
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174 |
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175 ggplot(score, aes(x = order, y = score)) + |
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176 geom_line() + |
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177 geom_segment(x = 0, xend = max(score$order[score$signature == "LOW"]), y = mean(score$score), yend = mean(score$score)) + |
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178 geom_area(aes(fill = signature), alpha = .7) + |
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179 scale_fill_manual(values=c("#ff0000", "#08661e")) + |
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180 geom_text(aes(x = 1, y = mean(score)), label = "Mean", vjust = -0.3, colour = "black") + |
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181 labs(title = "Ordered cell signature scores", x = "Cell index", y = "Score") |
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182 |
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183 density_score <- density(score$score) |
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184 ggplot(data.frame(density_score[1:2]), aes(x, y, fill = ifelse(x < mean(score$score), "LOW", "HIGH"))) + |
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185 geom_line() + |
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186 geom_vline(xintercept = mean(score$score)) + |
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187 geom_text(x = mean(score$score), y = max(density_score$y), label = "Mean", hjust = -0.3, colour = "black") + |
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188 geom_area(alpha = .7) + |
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189 scale_fill_manual(values=c("#ff0000", "#08661e")) + |
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190 ylim(0, max(density_score$y)) + |
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191 labs( |
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192 title = "Distribution of Cell signature scores", |
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193 x = paste("N =", density_score$n, "Bandwidth =", density_score$bw), |
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194 y = "Density", |
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195 fill = "Signature" |
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196 ) |
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197 |
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198 # Check score independant of low expression |
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199 p_gene <- ggplot(signature_output, aes(rate, nGenes)) + |
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200 geom_violin(aes(fill = rate), alpha = .5, trim = F, show.legend = F) + |
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201 scale_fill_manual(values=c("#ff0000", "#08661e")) + |
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202 geom_jitter() + labs(y = "Number of detected genes", x = "Signature") |
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203 |
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204 p_counts <- ggplot(signature_output, aes(rate, total_counts)) + |
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205 geom_violin(aes(fill = rate), alpha = .5, trim = F, show.legend = F) + |
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206 scale_fill_manual(values=c("#ff0000", "#08661e")) + |
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207 geom_jitter() + labs(y = "Total counts", x = "Signature") |
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208 |
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209 grid.arrange(p_gene, p_counts, ncol = 2, top = "Influence of library sequencing depth on cell signature scores") |
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210 |
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211 dev.off() |
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212 |
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213 # Save file |
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214 write.table( |
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215 signature_output, |
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216 opt$output, |
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217 sep = "\t", |
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218 quote = F, |
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219 col.names = T, |
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220 row.names = F |
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221 ) |
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222 |
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223 write.table( |
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224 statistics, |
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225 opt$stats, |
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226 sep = "\t", |
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227 quote = F, |
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228 col.names = T, |
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229 row.names = F |
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230 ) |