remove_nonexp {BioNERO} | R Documentation

## 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)

[Package BioNERO version 1.0.4 Index]