clusterExpr {CHARGE} | R Documentation |
Performs a partitioning clustering analysis in order to predict which samples have an enrichment for a genomic region of interest.
clusterExpr(se, cvExpr, threshold = NULL)
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. |
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.
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.
Benjamin Mayne
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