importGtf: importGtf

Description Usage Arguments Value Examples

View source: R/report_functions.R

Description

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

Usage

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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

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#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. 1, 2018, 2:54 a.m.