pcaExpr: pcaExprs

Description Usage Arguments Details Value Author(s) Examples

View source: R/pcaExpr.R

Description

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

Usage

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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

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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.