easyRNASeq-annotation-internal-methods: Internal easyRNASeq annotation methods

In easyRNASeq: Count summarization and normalization for RNA-Seq data

Description

These are internal methods used to retrieve annotations tabularll .getBmRangeUse biomaRt to get exon annotations. .getGffRangeUse Genome_intervals_stranded to get annotation from a gff file. .getGtfRangeUse Genome_intervals_stranded to get annotation from a gtf file. .geneModelAnnotationUse the provided exon annotation to define gene models. .readGffGtfUse Genome_intervals_stranded to get annotation from a gff or gtf file. It is called from getGffRange and getGtfRange.

Usage

.getBmRange(obj, ...)

Arguments

obj	an AnnotParam object containing the necessary retrieval information (datasource and type)
...	Additional arguments, passed to more internal functions.
annotation.type	describes the kind of annotation to keep the information from in a gtf or gff file. If set to NULL all the annotations are returned.
fields	added a parameter that allows defining the fields parsed from a gtf file. Still internal, but could easily be externalized.
filename	filename that contains the annotations
format	describes the kind of annotation provided. One of gtf or gff.
gAnnot	a GRanges object containing exon annotations
nbCore	number of CPU cores to use

Details

To use multicore machines more efficiently, the default parallel package will be used to parallelize the processing.

Value

A GRanges containing the loaded or processed annotations.

Author(s)

Nicolas Delhomme

easyRNASeq documentation built on April 30, 2020, 2 a.m.