prepareCDS {ribosomeProfilingQC} | R Documentation |
Prepare CDS library from a TxDb object.
prepareCDS(txdb, withUTR = FALSE)
txdb |
A TxDb object. |
withUTR |
Including UTR information or not. |
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;
library(GenomicFeatures) txdb_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(txdb_file) CDS <- prepareCDS(txdb)