cvExpr: cvExpr

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

Description

Calculates the coefficient of variation for each gene within a defined genomic region.

Usage

cvExpr(se, region)

Arguments

se	A SummarizedExperiment containing the normalised gene expression data.
region	A GRanges object containing the genomic location of the region of interest. This can either be an entire length or the subset of a chromosome.

Details

Calculates the coefficient of variation (CV) for each gene with a genomic region of interest. The CV Values can be used to determine which genes are not critical for appropiate clustering and can be filtered out prior to clustering.

Value

Returns a list containing the CV of each gene and the the quantile threshold of the data.

Author(s)

Benjamin Mayne

Examples

library(GenomicRanges)
data(datExprs)
chr21 <- GRanges("21:1-46709983")
cvExpr.out <- cvExpr(se = datExprs, region = chr21)

BenjaminAdelaide/CHARGE documentation built on May 14, 2019, 6:04 a.m.