importGtf {RCAS} | R Documentation |
This function uses rtracklayer::import.gff()
function to import genome
annoatation data from an Ensembl gtf file
importGtf( filePath, saveObjectAsRds = TRUE, readFromRds = TRUE, overwriteObjectAsRds = FALSE, keepStandardChr = TRUE, ... )
filePath |
Path to a GTF file |
saveObjectAsRds |
TRUE/FALSE (default:TRUE). If it is set to TRUE, a GRanges object will be created and saved in RDS format (<filePath>.granges.rds) so that importing can re-use this .rds file in next run. |
readFromRds |
TRUE/FALSE (default:TRUE). If it is set to TRUE, annotation data will be imported from previously generated .rds file (<filePath>.granges.rds). |
overwriteObjectAsRds |
TRUE/FALSE (default:FALSE). If it is set to TRUE, existing .rds file (<filePath>.granges.rds) will overwritten. |
keepStandardChr |
TRUE/FALSE (default:TRUE). If it is set to TRUE,
|
... |
Other arguments passed to rtracklayer::import.gff function |
A GRanges
object containing the coordinates of the annotated
genomic features in an input GTF file
#import the data and write it into a .rds file ## Not run: importGtf(filePath='./Ensembl75.hg19.gtf') ## End(Not run) #import the data but don't save it as RDS ## Not run: importGtf(filePath='./Ensembl75.hg19.gtf', saveObjectAsRds = FALSE) ## End(Not run) #import the data and overwrite the previously generated ## Not run: importGtf(filePath='./Ensembl75.hg19.gtf', overwriteObjectAsRds = TRUE) ## End(Not run)