peeling {dinamic}

Apply the peeling procedure at a given marker

Description

Apply the peeling procedure at a given marker

Usage

peeling(x, marker.data, cytoband, k)

Arguments

x

An n by m numeric matrix containing DNA copy number data from n subjects at m markers.

marker.data

marker.data A two-column numeric matrix of marker position data for markers in the autosomes. Column 1 contains the chromosome number for each marker, and column 2 contains the position (in base pairs) for each markers. This is a submatrix of the marker position matrix used by quickLook and detailedLook.

cytoband

A character vector of length m that contains the chromosome arm (p or q) for each marker. This is produced by the makeCytoband function.

k

A positive integer between 1 and m that represents the most aberrant marker.

Details

The peeling procedure is detailed in Algorithm 2 of Bioinformatics (2011) 27(5) 678 - 685, but here we provide a brief overview. By construction, marker k represents the most aberrant gain (loss). The peeling procedure rescales all copy number values in x that contribute to making marker k aberrant, so that after applying the peeling procedure marker k is "null." By construction, the rescaling procedure is restricted to entries in x that correspond to markers in the same chromosome arm as k. This allows users to assess the statistical significance of multiple gains (losses) throughout the genome.

Value

A list containing two components: (1) the n by m matrix produced by applying the peeling algorithm to the matrix x at marker k, and (2) the peak interval around marker k, as described in Bioinformatics (2011) 27(5) 678 - 685.