filter.exons {metaseqR} | R Documentation

## Filter gene expression based on exon counts

### Description

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

### Usage

        filter.exons(the.counts, gene.data, sample.list,
            exon.filters, restrict.cores = 0.8)

### Arguments

`the.counts` | a named list created with the `construct.gene.model` function. See its help page for details.
`gene.data` | an annotation data frame usually obtained with `get.annotation` containing the unique gene accession identifiers.
`sample.list` | the list containing condition names and the samples under each condition.
`exon.filters` | a named list with exon filters and their parameters. See the main help page of `metaseqr` for details.
`restrict.cores` | in case of parallel execution of several subfunctions, the fraction of the available cores to use. In some cases if all available cores are used (`restrict.cores=1` and the system does not have sufficient RAM, the running machine might significantly slow down.

### Value

a named list with two members. The first member (`result` is a named list whose names are the exon filter names and its members are the filtered rownames of `gene.data`. The second 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("hg19.exon.data",package="metaseqR")
    exon.counts <- hg19.exon.counts
    gene.data <- get.annotation("hg19","gene")
    sample.list <- sample.list.hg19
    exon.filters <- get.defaults("exon.filter")
    the.counts <- construct.gene.model(exon.counts,sample.list,
        gene.data)
    filter.results <- filter.exons(the.counts,gene.data,
        sample.list,exon.filters)

[Package metaseqR version 1.28.0 Index]