Mercurial > repos > morinlab > correct_read_counter

annotate correctReads.R @ 0:75c4a4c32bae draft default tip

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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
author morinlab
date Tue, 11 Oct 2016 14:18:25 -0400
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75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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diff changeset
1 library(TitanCNA)
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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2 version <- "0.1.1"
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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3 args <- commandArgs(TRUE)
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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4
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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5 tumWig <- args[1]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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6 normWig <- args[2]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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7 gc <- args[3]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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8 map <- args[4]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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9 target_list <- args[5]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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10 outfile <- args[6]
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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12 message('titan: Correcting GC content and mappability biases...')
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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14 if( !is.null(target_list) ){
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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15 target_list_data <- read.table(target_list, sep="\t", header=F, stringsAsFactors=F)
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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16 cnData <- correctReadDepth(tumWig, normWig, gc, map, targetedSequence = target_list_data)
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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17 } else {
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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18 cnData <- correctReadDepth(tumWig, normWig, gc, map)
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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19 }
75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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75c4a4c32bae planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/correct_read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
morinlab
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21 write.table(cnData, file = outfile, col.names = TRUE, row.names = FALSE, quote = FALSE, sep ="\t")