remove_nonexp {BioNERO} | R Documentation |
Remove genes that are not expressed based on a user-defined threshold
remove_nonexp( exp, method = "median", min_exp = 1, min_percentage_samples = 0.25 )
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. |
Filtered gene expression data frame or 'SummarizedExperiment' object.
Fabricio Almeida-Silva
data(zma.se) filt_exp <- remove_nonexp(zma.se, min_exp = 5)