remove_nonexp: Remove genes that are not expressed based on a user-defined...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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

Description

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.

Author(s)

Fabricio Almeida-Silva

See Also

rowMedians goodSamplesGenes

Examples

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

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.