Mercurial > repos > artbio > gsc_scran_normalize

annotate scran-normalize.R @ 0:9e2b0debeaea draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
author artbio
date Thu, 26 Sep 2019 10:50:32 -0400
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9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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diff changeset
1 # load packages that are provided in the conda env
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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2 options( show.error.messages=F,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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3 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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5 warnings()
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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6
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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7 library(optparse)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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8 library(scran)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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9
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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10 #Arguments
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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11 option_list = list(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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12 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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13 c("-d", "--data"),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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14 default = NA,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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15 type = 'character',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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16 help = "Input file that contains count values to transform"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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17 ),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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18 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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19 c("-s", "--sep"),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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20 default = '\t',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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21 type = 'character',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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22 help = "File separator [default : '%default' ]"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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23 ),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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24 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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25 "--cluster",
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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26 default=FALSE,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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27 action="store_true",
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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28 type = 'logical',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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29 help = "Whether to calculate the size factor per cluster or on all cell"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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30 ),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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31 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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32 c("-m", "--method"),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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33 default = 'hclust',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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34 type = 'character',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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35 help = "The clustering method to use for grouping cells into cluster : hclust or igraph [default : '%default' ]"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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36 ),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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37 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
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38 "--size",
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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39 default = 100,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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40 type = 'integer',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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41 help = "Minimal number of cells in each cluster : hclust or igraph [default : '%default' ]"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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42 ),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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43 make_option(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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44 c("-o", "--out"),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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45 default = "res.tab",
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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46 type = 'character',
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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47 help = "Output name [default : '%default' ]"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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48 )
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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49 )
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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50
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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51 opt = parse_args(OptionParser(option_list = option_list),
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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52 args = commandArgs(trailingOnly = TRUE))
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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53
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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54 if (opt$sep == "tab") {opt$sep = "\t"}
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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55
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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56 data = read.table(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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57 opt$data,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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58 check.names = FALSE,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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59 header = TRUE,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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60 row.names = 1,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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61 sep = opt$sep
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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62 )
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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63
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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64 ## Import data as a SingleCellExperiment object
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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65 sce <- SingleCellExperiment(list(counts=as.matrix(data)))
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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66
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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67
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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68 if(opt$cluster){
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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69 clusters <- quickCluster(sce, min.size = opt$size, method = opt$method)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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70
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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71 ## Compute sum factors
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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72 sce <- computeSumFactors(sce, cluster = clusters)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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73 } else {
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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74
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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75 ## Compute sum factors
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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76 sce <- computeSumFactors(sce)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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77 }
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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78
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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79 sce <- normalize(sce)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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80
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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81 logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits=5), check.names = F)
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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82
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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83
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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84 write.table(
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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85 logcounts,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
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diff changeset
86 opt$out,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
parents:
diff changeset
87 col.names = T,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
parents:
diff changeset
88 row.names = F,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
parents:
diff changeset
89 quote = F,
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
parents:
diff changeset
90 sep = "\t"
9e2b0debeaea "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit ddcf915dd9b690d7f3876e08b939adde36cbb8dd"
artbio
parents:
diff changeset
91 )