importGFF: importGFF

In fischuu/GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

importGFF

Description

Import a GFF file

Usage

importGFF(
  file,
  skip = "auto",
  nrow = -1,
  use.data.table = TRUE,
  level = "gene",
  features = NULL,
  num.features = c("FPKM", "TPM"),
  print.features = FALSE,
  merge.feature = NULL,
  merge.all = TRUE,
  class.names = NULL,
  verbose = TRUE
)

Arguments

file	file or folder
skip	numeric, lines to skip
nrow	numeric, lines to read
use.data.table	logical
level	Character, read level, default: "gene"
features	features to import
num.features	names of the numeric features
print.features	Logical, print available features
merge.feature	Character, merge multiple samples to dataset
merge.all	Logical, shall all samples be merged together
class.names	Definition of class name sin V9
verbose	Logical, verbose function output

Details

This function imports a standard gff file.

Value

A gff object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.gff", package="GenomicTools.fileHandler")
 # Import the example gff file  
   importGFF(fpath)
   

fischuu/GenomicTools.fileHandler documentation built on Feb. 15, 2025, 1:11 p.m.