clusterExpr: clusterExpr

In CHARGE: CHARGE: CHromosome Assessment in R from Gene Expression data

Description

Performs a partitioning clustering analysis in order to predict which samples have an enrichment for a genomic region of interest.

Usage

clusterExpr(se, cvExpr, threshold = NULL)

Arguments

se	A SummarizedExperiment containing the normalised gene expression data.
cvExpr	The output from cvExpr.
threshold	Optional. The quantile threshold of genes to be used for clustering analaysis. Default is NULL.

Details

Performs a partitioning clustering to predict which samples have a genomic duplication or deletion of a genomic region of interest. Samples are labelled Hyperploidy or Hypoploidy with respect to one another which are arbitrary labels referring to an enrichment or loss of genomic region.

Value

Returns a SummarizedExperiment containing the original inputted se, but where an additional column labelled Ploidy has been added into the meta data containing the classification of each sample.

Author(s)

Benjamin Mayne

Examples

library(SummarizedExperiment)
library(GenomicRanges)
data(datExprs)
chr21 <- GRanges("21:1-46709983")
cvExpr.out <- cvExpr(se = datExprs, region = chr21)
datExprs <- clusterExpr(se = datExprs, cvExpr = cvExpr.out, threshold = "25%")
colData(datExprs)$Ploidy

CHARGE documentation built on April 28, 2020, 6:06 p.m.