filter.genes {metaseqR} | R Documentation

## Filter gene expression based on gene counts

### Description

This function performs the gene expression filtering based on gene read counts and a set of gene filter rules. For more details see the main help pages of `metaseqr`.

### Usage

        filter.genes(gene.counts, gene.data, gene.filters,
        sample.list)

### Arguments

`gene.counts` | a matrix of gene counts, preferably after the normalization procedure.
`gene.data` | an annotation data frame usually obtained with `get.annotation` containing the unique gene accession identifiers.
`gene.filters` | a named list with gene filters and their parameters. See the main help page of `metaseqr` for details.
`sample.list` | the list containing condition names and the samples under each condition.

### Value

a named list with three members. The first member (`result` is a named list whose names are the gene filter names and its members are the filtered rownames of `gene.data`. The second member (`cutoff` is a named list whose names are the gene filter names and its members are the cutoff values corresponding to each filter. The third member is a matrix of binary flags (0 for non-filtered, 1 for filtered) for each gene. The rownames of the flag matrix correspond to gene ids.

### Author(s)

Panagiotis Moulos

### Examples

    data("mm9.gene.data",package="metaseqR")
    gene.counts <- mm9.gene.counts
    sample.list <- sample.list.mm9
    gene.counts <- normalize.edger(as.matrix(gene.counts[,9:12]),
        sample.list)
    gene.data <- get.annotation("mm9","gene")
    gene.filters <- get.defaults("gene.filter","mm9")
    filter.results <- filter.genes(gene.counts,gene.data,
        gene.filters,sample.list)

[Package metaseqR version 1.28.0 Index]