loadTxdb: General loader for txdb

Description Usage Arguments Value Examples

Description

Useful to allow fast TxDb loader like .db

Usage

1
loadTxdb(txdb, chrStyle = NULL)

Arguments

txdb

a TxDb file, a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite) or an ORFik experiment

chrStyle

a GRanges object, TxDb, FaFile, or a seqlevelsStyle (Default: NULL) to get seqlevelsStyle from. Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

Value

a TxDb object

Examples

1
2
3
4
5
library(GenomicFeatures)
# Get the gtf txdb file
txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                        package = "GenomicFeatures")
txdb <- loadDb(txdbFile)

ORFik documentation built on March 27, 2021, 6 p.m.