importGTF: Import a GTF File

Description Usage Arguments Details Value Author(s)

View source: R/importGTF.R

Description

This function imports a gtf file.

Usage

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  importGTF(file, skip = 5, nrow = -1, use.data.table = TRUE, level = "gene",
            features = NULL, print.features=FALSE)

Arguments

file

File name of the gtf file.

skip

Rows to skip from the top (usualy the number of header rows.

nrow

Total amount of rows read.

use.data.table

Logical, shall the data.table package be used for importing the GTF file.

level

Filter for the GTF Entry.

features

Features to extract from column #9.

print.features

logical, shall a list of availbe features be printed.

Details

This function imports a standard gtf file as provided by Ensembl. The current settings shouldn't be changed and the only the filename file should be provided. Hence, this function works currently only on the gene level.

Value

A data table of class gtf containing the columns of the gtf file, including the splitted last column.

Author(s)

Daniel Fischer


GenomicTools documentation built on July 12, 2017, 1:01 a.m.