Remove genes that are not expressed based on a user-defined threshold

Remove genes that are not expressed based on a user-defined threshold

Usage

remove_nonexp(
  exp,
  method = "median",
  min_exp = 1,
  min_percentage_samples = 0.25
)

Arguments

exp

A gene expression data frame with genes in row names and samples in column names or a `SummarizedExperiment` object.

method

Criterion to filter non-expressed genes out. One of "mean", "median", "percentage", or "allsamples". Default is "median".

min_exp

If method is 'mean', 'median', or 'allsamples', the minimum value for a gene to be considered expressed. If method is 'percentage', the minimum value each gene must have in at least n percent of samples to be considered expressed.

min_percentage_samples

In case the user chooses 'percentage' as method, expressed genes must have expression >= min_exp in at least this percentage. Values must range from 0 to 1.

Value

Filtered gene expression data frame or `SummarizedExperiment` object.

See also

rowMedians goodSamplesGenes

Author

Fabricio Almeida-Silva

Examples

data(zma.se)
filt_exp <- remove_nonexp(zma.se, min_exp = 5)