gff3_preprocess: =========================================================================...

In CyanolabFreiburg/rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

========================================================================= gff3_preprocess

gff3_preprocess process gff3 file from database for multiple usage

Description

gff3_preprocess processes the gff3 file extracting gene names and locus_tag from all coding regions (CDS), UTRs/ncRNA/asRNA are also extracted if available.

Usage

gff3_preprocess(path)

Arguments

path	path: path to the directory containing the gff3 file.

Details

The resulting dataframe contains region, positions, strand, gene and locus_tag.

Value

A list with 2 items:

data annotation:

region:

String, the region from the gff file

start:

Integer, the start of the annotation

end:

Integer, the end of the annotation

strand:

Boolean, the strand of the annotation

gene:

String, the annotated gene name

locus_tag:

String, the annotated locus tag

genome length:

a numeric vector containing the length of the genome

Examples

gff3_preprocess(
path = gzfile(system.file("extdata", "gff_e_coli.gff3.gz", package = "rifi"))
)

CyanolabFreiburg/rifi documentation built on May 7, 2023, 7:53 p.m.