REFCDS: REFCDS, build reference regions for CDS of protein coding...

In APAlyzer: A toolkit for APA analysis using RNA-seq data

Description

Build CDS reference for protein coding genes.

Usage

    REFCDS(txdb,IDDB)

Arguments

txdb	a TranscriptDb generate using GenomicFeatures
IDDB	Genome annotation of the corresponding species, e.g., "org.Hs.eg.db"

Value

The function REFCDS() returns a genomic ranges of CDS regions for each coding gene

Author(s)

Ruijia Wang

Examples

## build Reference ranges for CDS in mouse coding genes
    library("GenomicFeatures")
    library("org.Mm.eg.db")
    extpath = system.file("extdata", "mm9.chr19.refGene.R.DB", package="APAlyzer")
    txdb = loadDb(extpath, packageName='GenomicFeatures')
    IDDB = org.Mm.eg.db
    CDSdbraw = REFCDS(txdb,IDDB)

APAlyzer documentation built on Nov. 8, 2020, 4:54 p.m.