getSimilarities.sample: Get similarity metrics per sample

In macintyrelab/CNpare: Comparing tumour copy number profiles

Get similarity metrics per sample

Description

This function get similarity metrics for comparisons per sample

Usage

getSimilarities.sample(s, dat1, dat2, method, pvalue)

Arguments

s	sample name
dat1	matrix with bin-level copy numbers per sample to test
dat2	matrix with bin-level copy numbers per model to compare
method	method to use for testing similarity. Default is all methods.
pvalue	a logical value to indicate if the empirical pvalue is calculated or not

Value

dataframe with similarity metrics for all comparisons of the sample

Examples

posBins<-lapply(1,function(chr)
    getBinsStartsEnds(window=1000000, chr, lengthChr[chr]))
ccle_cn<-getCNbins(posBins=posBins,data=cells_segcn,samples=unique(cells_segcn$sample)[1:2])
exp_cell<-as.matrix(ccle_cn[,1])
colnames(exp_cell)<-unique(cells_segcn$sample)[1]
measures<-getSimilarities.sample(s=colnames(exp_cell),dat1=exp_cell,
    dat2=ccle_cn,method="pearson",pvalue=FALSE)

macintyrelab/CNpare documentation built on April 15, 2022, 4:46 a.m.