importGtf: importGtf

In RCAS: RNA Centric Annotation System

Description

This function uses rtracklayer::import.gff() function to import genome annoatation data from an Ensembl gtf file

Usage

importGtf(
  filePath,
  saveObjectAsRds = TRUE,
  readFromRds = TRUE,
  overwriteObjectAsRds = FALSE,
  keepStandardChr = TRUE,
  ...
)

Arguments

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, seqlevelsStyle will be converted to 'UCSC' and keepStandardChromosomes function will be applied to only keep data from the standard chromosomes.
...	Other arguments passed to rtracklayer::import.gff function

Value

A GRanges object containing the coordinates of the annotated genomic features in an input GTF file

Examples

#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)

RCAS documentation built on Nov. 8, 2020, 8:03 p.m.