removeGapSpanningSegments: removes segments that span a reference assembly gap

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

Description

intersects alterations with a bed file of reference assembly gap and removes regions that overlap, by default, at least 75% with one of these gaps. This has proven to be a reliable indicator of false-positive calls.

Usage

  removeGapSpanningSegments(segs,rdo,maxOverlap=0.75,gapExpansion=1.0)

Arguments

rdo	a readDepth object created with new("rdObject") and filled with read counts using the getReadDepth() command (optionally corrected first)
segs	a data frame of altered segments returned by cnSegments() or cnSegments.paired(), then filtered to contain only alterations by getAlts().
maxOverlap	if a segment overlaps at least this much with a gap, it will be removed.
gapExpansion	expand each gap feature by this fraction before doing gap filtering. A value of 1.3 would expand each gap by 30

Value

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

See Also

'readDepth'

Examples

  #create a rdObject, set bin params
  #  x <- new("rdObject")

  #fill the bins with reads
  #  x.reads <- readDepth(x)

  #do gc correction on the read counts
  #  x.gcCorr <- rd.gcCorrect(x)

  #return regions of CN gain and loss
  #  segs <- rd.cnSegments(x.gcCorr)

  #get alterations
  #  alts = getAlts(segs,rdo)

  #filter them
  #  alts = removeGapSpanningSegments(segs,rdo,maxOverlap=0.75)

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