Filter genes that have less than a minimum threshold CPM for a given group/tissue — filterLowGenes • netZooR

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')