filter_RNA_seq {GWENA} | R Documentation

## Filtering of low counts

### Description

Keeping genes with at least one sample with count above min_count in RNA-seq data.

### Usage

    filter_RNA_seq(
      data_expr,
      min_count = 5,
      method = c("at least one", "mean", "all")
    )

### Arguments

`data_expr` | matrix or data.frame or SummarizedExperiment, table of expression values (either microarray or RNA-seq), with genes as column and samples as row.
`min_count` | integer, minimal number of count to be considered in method.
`method` | string, name of the method for filtering. Must be one of "at least one", "mean", or " all"

### Details

Low counts in RNA-seq can bring noise to gene co-expression module building, so filtering them help to improve quality.

### Value

A data.frame of filtered genes

### Examples

    df <- matrix(abs(rnorm(15*45)), 15) * 3
    colnames(df) <- paste0("gene_", seq_len(ncol(df)))
    rownames(df) <- paste0("sample_", seq_len(nrow(df)))
    df_filtered <- filter_RNA_seq(df)

[Package GWENA version 1.2.0 Index]