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

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

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')

yarn documentation built on Nov. 8, 2020, 7:50 p.m.