Man pages for chrisamiller/copyCat
Find regions of genomic copy number loss and gain from short reads

addBinsdumpParams
cnNeutralDepthFromHetSitescnNeutralDepthFromHetSites
cnSegmentsIdentifies regions of copy-number alteration
cnSegments.pairedIdentifies regions of differential copy-number alteration...
copyCat-packageUses the depth of short reads in windows across the genome to...
functionsreadDepth Functions
gcCorrectreadDepth: GC-content correction
getAltsgetAlts
getReadDepthgetReadDepth
mapCorrectCorrect read depth for mapability
mergeSegsmergeSegs
plotSegsplotSegs
rdObject-classClass "rdObject" ~~~
refineBreakpointsrefine edges of CNAs by matching them with nearby breakpoints
removeCoverageArtifactsremove alterations with extremely high or low coverage in...
removeGapSpanningSegmentsremoves segments that span a reference assembly gap
subtractBinssubtractBins
trimSegmentEndstrimSegmentEnds
writeAltswriteAlts
writeSegswriteSegs
writeThresholdswriteThresholds
chrisamiller/copyCat documentation built on Dec. 2, 2017, 4:28 a.m.