filterLowGenes: Filter genes that have less than a minimum threshold CPM for...

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Filter genes that have less than a minimum threshold CPM for a given group/tissue

Description

Filter genes that have less than a minimum threshold CPM for a given group/tissue

Usage

filterLowGenes(obj, groups, threshold = 1, minSamples = NULL, ...)

Arguments

obj	ExpressionSet object.
groups	Vector of labels for each sample or a column name of the phenoData slot. for the ids to filter. Default is the column names.
threshold	The minimum threshold for calling presence of a gene in a sample.
minSamples	Minimum number of samples - defaults to half the minimum group size.
...	Options for cpm.

Value

Filtered ExpressionSet object

See Also

cpm function defined in the edgeR package.

Examples

data(skin)
filterLowGenes(skin,'SMTSD')

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.