filterByExpr {edgeR}R Documentation

Filter Genes By Expression Level

Description

Determine which genes have sufficiently large counts to be retained in a statistal analysis.

Usage

## S3 method for class 'DGEList'
filterByExpr(y, design = NULL, group = NULL, lib.size = NULL, ...)
## Default S3 method:
filterByExpr(y, design = NULL, group = NULL, lib.size = NULL,
             min.count = 10, min.total.count = 15, ...)

Arguments

y

matrix of counts or a DGEList object.

design

design matrix. Ignored if group is not NULL.

group

vector or factor giving group membership for a oneway layout, if appropriate.

lib.size

library size, defaults to colSums(y).

min.count

numeric. Minimum count required for at least some samples.

min.total.count

numeric. Minimum total count required.

...

any other arguments. For the DGEList methods, other arguments will be passed to the default method. For the default method, other arguments are not currently used.

Value

Logical vector of length nrow(y) indicating which rows of y to keep in the analysis.

Author(s)

Gordon Smyth

Examples

## Not run: 
keep <- filterByExpr(y)
y <- y[keep,]

## End(Not run)

[Package edgeR version 3.20.9 Index]