metaseqR (version 1.12.2)

construct.gene.model: Assemble a gene model based on exon counts

Description

This function assembles gene models (single genes, not isoforms) based on the input exon read counts file and a gene annotation data frame, either from an external file provided by the user, or with the get.annotation function. The gene.data argument should have a specific format and for this reason it's better to use one of the two aforementioned ways to supply it. This function is intended mostly for internal use but can be used if the requirements are met.

Usage

construct.gene.model(exon.counts, sample.list, gene.data,
        multic = FALSE)

Arguments

exon.counts

the exon counts data frame produced by reading the exon read counts file.

sample.list

the list containing condition names and the samples under each condition.

gene.data

an annotation data frame from the same organism as exon.counts (such the ones produced by get.annotation).

multic

a logical value indicating the presence of multiple cores. Defaults to FALSE. Do not change it if you are not sure whether package multicore has been loaded or not.

Value

• A named list where names represent samples. Each list member is a also a named list where names correspond to gene ids and members are named vectors. Each vector is named according to the exons corresponding to each gene and contains the read counts for each exon. This structure is used for exon filtering and assembling final gene counts in the metaseqr pipeline.

Examples

# Takes some time to run...
data("hg19.exon.data",package="metaseqR")
gene.data <- get.annotation("hg19","gene","ensembl")
reduced.gene.data <- reduce.gene.data(hg19.exon.counts,
    gene.data)
multic <- check.parallel(0.4)
gene.model <- construct.gene.model(hg19.exon.counts,
    sample.list.hg19,gene.data,multic)