processExons {Rsubread} | R Documentation

## Obtain Chromosomal Coordiates of Each Exon Using NCBI Annotation

### Description

This is for internal use. It converts the NCBI exon annotations into data files for use in the `detectionCall` function.

### Usage

    processExons(

        filename = "human_seq_gene.md",
        species = "hg")

### Arguments

`filename` | a character string giving the name of input .md file (NCBI annotation file)
`species` | a character string specifying the species

### Details

This is an internal function and should not be called by users directly.

It processes annotation of genes in human genome GRCh37/hg19 or mouse genome GRCm37/mm9. The annotation is available for download from the following links (these annotations include chromosomal coordinates of UTR and CDS regions of genes):

ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.2/mapview/seq_gene.md.gz

ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/mapview/seq_gene.md.gz

This function finds the chromosomal coordinates of intergenic regions (regions between neighbouring genes) and then outputs them to a file. It also outputs to a file chromosomal coordinates of exons of genes by concatenating UTRs with CDSs and merging overlapping CDSs within each gene. The generated annotation files will then be used by `detectionCallAnnotation` function to produce annotation data required by `detectionCall` function.

### Value

Two annotation files are written to the current working directory. This function returns a `NULL` object.

### Author(s)

Zhiyin Dai and Wei Shi

[Package Rsubread version 2.4.3 Index]