... rtracklayer::import for signature "GFFFile,ANY,ANY" has an argument text, the help page says:
## S4 method for signature 'GFFFile,ANY,ANY'
import(con, format, text,
version = c("", "1", "2", "3"),
genome = NA, colnames = NULL, which = NULL,
feature.type = NULL, se ...
I encountered a really long elapsed time for importing a small toy gff3 file
when using `import.gff3()`, here is what I did:
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
> grl.exons = exonsBy(txdb, by = 'tx' ...
... For a GTF file downloaded from iGenome， say, hg19.gtf, a significant proportion of genes will be dropped without warning when use makeTxDbFromGFF to import it.
As I examined those genes in the source GTF file, I believe the genes with multiple chromosome locations (e.g. chr1 and chr2) will be dropp ...
... I encountered a problem regard to coordinate transformation when using tracks function in ggbio package. An example is here:
# Create a GRanges and plot it normally
gr = GRanges('chr2', IRanges(start = 50, end = 100))
p = ggplot(gr) + geom_rect()
# However, when it is wrapp ...