pcaExpr: pcaExprs

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

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%")

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