loadRegion {ORFik} | R Documentation |
Usefull to simplify loading of standard regions, like cds' and leaders. Adds another safety in that seqlevels will be set
loadRegion( txdb, part = "tx", names.keep = NULL, by = "tx", skip.optimized = FALSE )
txdb |
a TxDb file or a path to one of: (.gtf ,.gff, .gff2, .gff2, .db or .sqlite), if it is a GRangesList, it will return it self. |
part |
a character, one of: tx, ncRNA, mrna, leader, cds, trailer, intron, NOTE: difference between tx and mrna is that tx are all transcripts, while mrna are all transcripts with a cds, respectivly ncRNA are all tx without a cds. |
names.keep |
a character vector of subset of names to keep. Example: loadRegions(txdb, names = "ENST1000005"), will return only that transcript. Remember if you set by to "gene", then this list must be with gene names. |
by |
a character, default "tx" Either "tx" or "gene". What names to output region by, the transcript name "tx" or gene names "gene". NOTE: this is note the same as cdsBy(txdb, by = "gene"), cdsBy would then only give 1 cds per Gene, loadRegion gives all isoforms, but with gene names. |
skip.optimized |
logical, default FALSE. If TRUE, will not search for optimized rds files to load created from ORFik::makeTxdbFromGenome(..., optimize = TRUE). The optimized files are ~ 100x faster to load for human genome. |
Load as GRangesList if input is not already GRangesList.
a GrangesList of region
gtf <- system.file("extdata", "annotations.gtf", package = "ORFik") loadRegion(gtf, "cds") loadRegion(gtf, "intron")