absoluteCN {Repitools} | R Documentation |
This function uses the GCadjustCopy
function to convert
a matrix of count data into absolute copy number estimates, then it segments them,
and reports the copy number of either the input regions or user-defined regions of
interest.
## S4 method for signature 'data.frame,matrix,GCAdjustParams' absoluteCN(input.windows, input.counts, gc.params, ...) ## S4 method for signature 'GRanges,matrix,GCAdjustParams' absoluteCN(input.windows, input.counts, gc.params, segment.sqrt = TRUE, ..., verbose = TRUE)
input.windows |
A |
input.counts |
A matrix of counts. Rows are genomic windows and columns are samples. |
gc.params |
A |
segment.sqrt |
Whether to square root the absolute copy number estimates before running the segmentation. |
... |
For the |
verbose |
Whether to print the progess of processing. |
For details of the absolute copy number estimation step, see the documentation for
GCadjustCopy
.
For details of the segmentation, see segment
documentation.
By default, no weights are used.
A CopyEstimate
object. If regions
was not provided,
it describes the input windows, otherwise it describes the windows specified by
regions
.
Dario Strbenac
## Not run: library(BSgenome.Hsapiens.UCSC.hg18) library(BSgenome.Hsapiens36bp.UCSC.hg18mappability) load("inputsReads.RData") windows <- genomeBlocks(Hsapiens, chrs = paste("chr", c(1:22, 'X', 'Y'), sep = ''), width = 20000) counts <- annotationBlocksCounts(inputsReads, anno = windows, seq.len = 300) gc.par <- GCAdjustParams(genome = Hsapiens, mappability = Hsapiens36bp, min.mappability = 50, n.bins = 10, min.bin.size = 10, poly.degree = 4, ploidy = c(2, 4)) abs.cn <- absoluteCN(input.windows = windows, input.counts = counts, gc.params = gc.par) ## End(Not run)