clusterExpr {CHARGE} | R Documentation

## clusterExpr

### 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

[Package CHARGE version 1.2.0 Index]