importCustomAnnotation {sitadela} | R Documentation |
This function imports a custom GTF/GFF file in a manner helpful for the addition of custom annotations to sitadela.
importCustomAnnotation(gtfFile, metadata, type = c("gene", "transcript", "utr", "transexon", "transutr", "exon"))
gtfFile |
a GTF file containing the gene structure of the organism to be imported. |
metadata |
a list with additional information about
the annotation to be imported. The same as in the
|
type |
same as the |
The function returns a GenomicRanges
object with
the requested annotation.
Panagiotis Moulos
# Dummy GTF as example chromInfo <- data.frame(length=c(1000L,2000L,1500L), row.names=c("A","B","C")) # Build with the metadata list filled (you can also provide a version) if (.Platform$OS.type == "unix" && !grepl("^darwin",R.version$os)) { myGenes <- importCustomAnnotation( gtfFile=file.path(system.file(package="sitadela"), "dummy.gtf.gz"), metadata=list( organism="dummy", source="dummy_db", version=1, chromInfo=chromInfo ), type="gene" ) } ## Real data! ## Gene annotation dump from Ensembl #download.file(paste0("ftp://ftp.ensembl.org/pub/release-98/gtf/", # "dasypus_novemcinctus/Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"), # file.path(tempdir(),"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz")) ## Build with the metadata list filled (you can also provide a version) #dasGenes <- importCustomAnnotation( # gtfFile=file.path(tempdir(),"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"), # metadata=list( # organism="dasNov3_test", # source="ensembl_test" # ), # type="gene" #)