CNscore: CNomplexity::CNscore

Description Usage Arguments Details Value

View source: R/CNscore.R

Description

Score chromosomal level copy number changes.

Usage

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CNscore(segFiles,threshLow=0.275,
                      threshHigh=0.8,doRel=TRUE,
                      doCat=FALSE,doScale=FALSE,
			tumTotCol=7,normTotCol=5,
			startCol=3,endCol=4,chromCol=2,
			sampleCol=1,head=TRUE)

Arguments

segFiles

String or vector of strings. Path to segment files.

threshLow

Numeric. Threshold above which to call copy number gain or loss.

threshHigh

Numeric. Threshold above which to call extreme copy numebr gain or loss.

doRel

Boolean. Whether to adjust scores based on relative lengths of chromosomes.

doCat

Boolean. Whether to categorise copy number chaanges into chromosomal, arm-level, focal or large split.

doScale

Boolean. Whether to scale copy number scores.

tumTotCol

Integer. Seg column with total copy number information for tumour sample.

normTotCol

Integer. Seg column with total copy number information for matched normal sample.

startCol

Integer. Seg column with segment start positions.

endCol

Integer. Seg column with segment end positions.

chromCol

Integer. Seg column with segment chromosomes.

sampleCol

Integer. Seg column with sample names for each segment.

head

Boolean. Whether seg file has headers.

Details

Implements copy number scores from Davoli et al. (2017).

Value

Matrix of copy number categories if doCat=TRUE, or vector of copy number scores if doCat=FALSE.


SteeleCD/CNomplexity documentation built on May 29, 2019, 2:09 p.m.