prepareCDS: Prepare CDS

In ribosomeProfilingQC: Ribosome Profiling Quality Control

Description

Prepare CDS library from a TxDb object.

Usage

prepareCDS(txdb, withUTR = FALSE)

Arguments

txdb	A TxDb object.
withUTR	Including UTR information or not.

Value

A GRanges object with metadata which include: tx_id: transcript id; tx_name: transcript name; gene_id: gene id; isFirstExonInCDS: is first exon in CDS or not; idFirstExonInCDS: the id for the first exon; isLastExonInCDS: is last exon in CDS or not; wid.cumsu: cumulative sums of number of bases in CDS; internalPos: offset position from 1 base;

Examples

library(GenomicFeatures)
txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)
CDS <- prepareCDS(txdb)

ribosomeProfilingQC documentation built on March 13, 2021, 2:01 a.m.