degFilter {DEGreport} | R Documentation

## Filter genes by group

### Description

This function will keep only rows that have a minimum counts of 1 at least in a `min` number of samples (default 80%).

### Usage

    degFilter(counts, metadata, group, min = 0.8, minreads = 0)

### Arguments

`counts` | Matrix with expression data, columns are samples and rows are genes or other feature.
`metadata` | Data.frame with information about each column in counts matrix. Rownames should match `colnames(counts)`.
`group` | Character column in metadata used to group samples and applied the cutoff.
`min` | Percentage value indicating the minimum number of samples in each group that should have more than 0 in count matrix.
`minreads` | Integer minimum number of reads to consider a feature expressed.

### Value

count `matrix` after filtering genes (features) with not enough expression in any group.

### Examples

    data(humanGender)
    library(SummarizedExperiment)
    idx <- c(1:10, 75:85)
    c <- degFilter(assays(humanGender)[[1]][1:1000, idx],
      colData(humanGender)[idx,], "group", min=1)

[Package DEGreport version 1.28.0 Index]