importGFF {GenomicTools.fileHandler}

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)