absoluteCN: Calculate and Segment Absolute Copy Number from Sequencing...
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) Examples

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 `data.frame` with (at least) columns `chr`, `start`, and `end`, or a GRanges object.
`input.counts`	A matrix of counts. Rows are genomic windows and columns are samples.
`gc.params`	A `GCAdjustParams` object, holding parameters related to mappability and GC content correction of read counts.
`segment.sqrt`	Whether to square root the absolute copy number estimates before running the segmentation.
`...`	For the `data.frame` method; the `verbose` variable and any additional parameters to pass to the `segment` function. For the `GRanges` method; additional parameters for the segmentation.
`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)