refineBreakpoints: refine edges of CNAs by matching them with nearby breakpoints

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

Description

takes a readDepth object containing read counts and parameters, along with the results of CN segmentation, and refines the edges of the CN regions by matching them with nearby breakpoints.

Usage

  refineBreakpoints(rdo,segs)

Arguments

rdo	a readDepth object created with new("rdObject") and filled with read counts using the readDepth() command
segs	a data frame containing positions of copy number segments, as produced by the rd.cnSegment function

Details

Assumes a breakpoint list (in bed format) is present in the annotations directory (see manual)

If the region around the window contains more than one breakpoint, it is unable to determine which bp is correct and makes no adjustment

Value

returns a modified copy of the segs data frame that was fed in.

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.reads)

  ## map

  ## cn seg

  ##x.matchBreakpoints(x,segs)

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