easyRNASeq annotation internal methods {easyRNASeq} | R Documentation

## Internal easyRNASeq annotation methods

### Description

These are internal methods used to retrieve annotations tabularll `.getBmRange`Use `biomaRt` to get exon annotations. `.getGffRange`Use `Genome_intervals_stranded` to get annotation from a gff file. `.getGtfRange`Use `Genome_intervals_stranded` to get annotation from a gtf file. `.geneModelAnnotation`Use the provided exon annotation to define gene models. `.readGffGtf`Use `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

[Package easyRNASeq version 2.28.0 Index]