Man pages for chrisamiller/copyCat
Find regions of genomic copy number loss and gain from short reads
| addBins | dumpParams |
| cnNeutralDepthFromHetSites | cnNeutralDepthFromHetSites |
| cnSegments | Identifies regions of copy-number alteration |
| cnSegments.paired | Identifies regions of differential copy-number alteration... |
| copyCat-package | Uses the depth of short reads in windows across the genome to... |
| functions | readDepth Functions |
| gcCorrect | readDepth: GC-content correction |
| getAlts | getAlts |
| getReadDepth | getReadDepth |
| mapCorrect | Correct read depth for mapability |
| mergeSegs | mergeSegs |
| plotSegs | plotSegs |
| rdObject-class | Class "rdObject" ~~~ |
| refineBreakpoints | refine edges of CNAs by matching them with nearby breakpoints |
| removeCoverageArtifacts | remove alterations with extremely high or low coverage in... |
| removeGapSpanningSegments | removes segments that span a reference assembly gap |
| subtractBins | subtractBins |
| trimSegmentEnds | trimSegmentEnds |
| writeAlts | writeAlts |
| writeSegs | writeSegs |
| writeThresholds | writeThresholds |
