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

Description Usage Arguments Details Value Examples

Description

This function iteratively applies the peelingOne function, thereby identifying multiple

Usage

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peelingOneIterate(
  X,
  posDT,
  gain = TRUE,
  nullDist = NULL,
  threshold = NULL,
  numIters = 5
)

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.

gain

A logical value indicating whether gains (TRUE) or losses (FALSE) will be peeled.

Default = TRUE.

nullDist

An empirical null distribution produced by the cyclic shift algorithm.

Default = NULL.

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. Default = NULL.

numIters

The number of times peelingOne will be iterated. Default = 5.

Details

peaks across the genome in a single cohort. Gains and losses should be analyzed separately.

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"]]

 gain = TRUE

 nullDist = NULL

 threshold = NULL

 numIters = 3

 peeledLusc=peelingOneIterate(X=lusc,posDT=posDT,gain=TRUE,nullDist=NULL,threshold=NULL,numIters=3)   

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