genCNValignmentStats: generate alignments stats for BWA CNV alignments
In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions
View source: R/genCNValignmentStats.R
Description
generate alignments stats for BWA CNV alignments
Usage
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genCNValignmentStats(sid, bamDir, fqsDir, projName,
remRoot = file.path("/scratch/pschofield/Projects", projName),
outDir = "Analysis/mapping_stats", noSub = F, ncores = 1,
scpIt = T, mem = "32Gb",
samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", ufExt = ".bam",
mdExt = "_dedup.bam", rdExt = "_rmdup.bam")
Arguments
bamDir
directory of alignment files
PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.
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View source: R/genCNValignmentStats.R
Description
generate alignments stats for BWA CNV alignments
Usage
1 2 3 4 5 6 | genCNValignmentStats(sid, bamDir, fqsDir, projName,
remRoot = file.path("/scratch/pschofield/Projects", projName),
outDir = "Analysis/mapping_stats", noSub = F, ncores = 1,
scpIt = T, mem = "32Gb",
samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", ufExt = ".bam",
mdExt = "_dedup.bam", rdExt = "_rmdup.bam")
|
Arguments
bamDir |
directory of alignment files |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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