processExons: Obtain chromosomal coordiates of each exon using NCBI...

Description Usage Arguments Details Value Author(s)

View source: R/processExons.R

Description

This is for internal use.

Usage

1
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 the NCBI mapview annotation data downloaded 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/mapview/seq_gene.md.gz

ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/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


Rsubread documentation built on Nov. 9, 2018, 6 p.m.