read.annot.from.gff: Read a GFF file from NCBI and return a GRanges object.

In CONDOP: Condition-Dependent Operon Predictions

Description

Read a GFF file from NCBI and return a GRanges object.

Usage

read.annot.from.gff(gff.file, locus.tags = TRUE, nrows = -1,
  verbose = TRUE)

Arguments

gff.file	a GFF file
locus.tags	only return genes with locus tags. Defaults to TRUE.
nrows	number of rows to read.
verbose	Indicate whether information about the process should be reported. Defaults to TRUE.

Value

GRanges with 4 elementMetadata columns: locus, proetin id, gene id, feature, description and gene name. If all rows are returned (locus.tags=FALSE), then score, phase and tags are included.

Author(s)

Vittorio Fortino read.annot.from.gff()

CONDOP documentation built on May 2, 2019, 1:26 p.m.