Description Usage Arguments Details Value See Also Examples
View source: R/rd.breakpoints.R
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.
1 | rd.matchBreakpoints(rdo,segs)
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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 |
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
returns a modified copy of the segs data frame that was fed in.
'readDepth'
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ##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)
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