removeCoverageArtifacts: remove alterations with extremely high or low coverage in...

In chrisamiller/copyCat: Find regions of genomic copy number loss and gain from short reads

Description

Identifies alterations with coverage at least 10x higher or lower than the median depth in the normal sample, which are generally artifacts. Removes them

Usage

  removeCoverageArtifacts(segs, rdo)

Arguments

segs	a data frame of altered segments returned by cnSegments() or cnSegments.paired(), then filtered to contain only alterations by getAlts().
rdo	a readDepth object created with new("rdObject") and filled with read counts using the getReadDepth() command (optionally corrected first). This should be the object containing reads from the normal sample

Value

returns a dataframe with 5 columns: chr start stop num.probes copynumber

See Also

'readDepth'

Examples

  #  alts = removeCoverageArtifacts(segs,rdo)

chrisamiller/copyCat documentation built on July 20, 2021, 12:59 a.m.