processExons: Obtain Chromosomal Coordiates of Each Exon Using NCBI...
In Rsubread: Mapping, quantification and variant analysis of sequencing data

Description Usage Arguments Details Value Author(s)

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

processExons(

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

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

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.

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

Zhiyin Dai and Wei Shi

Rsubread documentation built on March 17, 2021, 6:01 p.m.