pcaExpr {CHARGE} | R Documentation

## pcaExprs

### Description

Creates a PCA plot using genes within a defined genomic region.

### Usage

    pcaExpr(se, cvExpr, threshold = NULL)

### Arguments

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

### Details

Performs a principle component analysis for a given gene expression data using only genes within a defined region.

### Value

Returns a PCA plot showing the seperation of samples that were labelled hyperploidy or hypoploidy in clusterExpr.

### Author(s)

Benjamin Mayne

### Examples

    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%")
    pcaExpr(se = datExprs, cvExpr = cvExpr.out, threshold = "25%")

[Package CHARGE version 1.4.0 Index]