peelingTwo: A Function to Apply the Peeling Algorithm in a Two Copy...

Description Usage Arguments Details Value Examples

View source: R/peelingTwo.R

Description

This function applies a modified version of the peeling algorithm originally described in Walter et al.,

Usage

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peelingTwo(X, Y, posDT, k, threshold = NULL)

Arguments

X

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

Y

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 and Y) containing the peak that will be peeled.

threshold

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

rowMeans(X) - rowMeans(Y) are less than threshold will not be peeled.

Details

(PMID 21183584) to remove a peak from the copy number differences and define a genomic interval of interest

around the peak.

Value

A list containing three elements: X, Y, and interval. X and Y are updated versions of the input copy number matrices X and Y 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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luad=pD[["X"]]

 lusc=pD[["Y"]]

 posDT=pD[["posDT"]]

 kDiff=which.max(rowMeans(luad)-rowMeans(lusc))

 peeledDiff=peelingTwo(X=luad,Y=lusc,posDT=posDT,k=kDiff,threshold=NULL)

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