expression_subset: Subset an ExpressionSet

In MahShaaban/aacna: Analysis Compendium of the Autophagy and AMPK Co-expression

Description

Subset an ExpressionSet object by row and/or column, and perform collapse of repeated probes corresponding to the same gene ID

Usage

expression_subset(eset, byrow, bycol, collapse_rows = FALSE, ...)

Arguments

eset	An ExpressionSet object
byrow	A logical vector masking rows of eset
bycol	A logical vector masking columns of eset
collapse_rows	A logical (default FALSE)
...	Other arguments passed to collapse_rows

Value

A tidy expression matrix. The dimensions of the matrix are either equal to the byrow and bycol argumnets when collapse_rows is FALSE, or equal the rowGroup and the bycol arguments otherwise

Examples

library(Biobase)
data("sample.ExpressionSet")

pd <- pData(sample.ExpressionSet)

set.seed(123)
byrow <- sample(c(TRUE, FALSE), nrow(sample.ExpressionSet), replace = TRUE)
bycol <- pd$sex == 'Female'

expression_subset(sample.ExpressionSet, byrow, bycol)

MahShaaban/aacna documentation built on May 17, 2019, 6:21 p.m.