loadTxdb: General loader for txdb

In JokingHero/ORFik: Open Reading Frames in Genomics

General loader for txdb

Description

Useful to allow fast TxDb loader like .db

Usage

loadTxdb(txdb, chrStyle = NULL, organism = NA, chrominfo = 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, , a seqlevelsStyle or Seqinfo. (Default: NULL) to get seqlevelsStyle from. In addition if it is a Seqinfo object, seqinfo will be updated. Example of seqlevelsStyle update: 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"
organism	character, default NA. Scientific name of organism. Only used if input is path to gff.
chrominfo	Seqinfo object, default NULL. Only used if input is path to gff.

Value

a TxDb object

Examples

library(GenomicFeatures)
# Get the gtf txdb file
txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                        package = "GenomicFeatures")
txdb <- loadTxdb(txdbFile)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.