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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')