peelingOne: A Function to Apply the Peeling Algorithm in a Single Copy...

Description Usage Arguments Details Value Examples

Description

This function applies the peeling algorithm, as described in Walter et al. (PMID 21183584),

Usage

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peelingOne(X, posDT, k, threshold = NULL)

Arguments

X

A matrix of normalized gene-level copy number data (rows = genes, columns = subjects).

posDT

A data frame containing genomic position information for the genes in X.

k

The location (row of X) containing the peak that will be peeled.

threshold

A tuning parameter that controls the size of the peeled region. Rows of X

with mean copy number less than threshold will not be peeled.

Details

to remove a peak from a copy number data set and define a genomic interval of interest around

the peak.

Value

A list containing two elements: X and interval. X is an updated version of the input copy number matrix in which the peak at k has been removed, and interval is genomic region containing k. By construction, interval cannot extend beyond the chromosome arm containing k.

Examples

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lusc=pD[["X"]]

 posDT=pD[["posDT"]]

 kLusc=which.max(rowMeans(lusc))

 peeledLusc=peelingOne(X=lusc,posDT=posDT,k=kLusc,threshold=NULL)   

DiNAMIC.Duo documentation built on Oct. 1, 2021, 1:08 a.m.