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

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

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')

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.