Assemble a gene model based on exon counts
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.
the exon counts data frame produced by reading the exon read counts file.
the list containing condition names and the samples under each condition.
an annotation data frame from the same
a logical value indicating the presence of
multiple cores. Defaults to
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.
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# 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)
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