pcaExpr {CHARGE} | R Documentation |
Creates a PCA plot using genes within a defined genomic region.
pcaExpr(se, cvExpr, threshold = NULL)
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. |
Performs a principle component analysis for a given gene expression data using only genes within a defined region.
Returns a PCA plot showing the seperation of samples that were labelled hyperploidy or hypoploidy in clusterExpr.
Benjamin Mayne
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%")