absoluteCN {Repitools} | R Documentation

## 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

      ## 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

      ## 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)

[Package Repitools version 1.28.0 Index]