Calculate and Segment Absolute Copy Number from Sequencing Counts

Description

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.

Usage

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  ## 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)

Arguments

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.

Details

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.

Value

A CopyEstimate object. If regions was not provided, it describes the input windows, otherwise it describes the windows specified by regions.

Author(s)

Dario Strbenac

Examples

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  ## 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)

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