metaseqR (version 1.12.2)

filter.exons: 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.

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)