clusterExpr: clusterExpr

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

1
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

1
2
3
4
5
6
7
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

BenjaminAdelaide/CHARGE documentation built on May 14, 2019, 6:04 a.m.