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PopGenome (version 2.1.6)

split_data_into_GFF_attributes: Split the data into GFF attributes

Description

Splits the data into GFF attributes defined by the user.

Usage

split_data_into_GFF_attributes(object, gff.file, chr, attribute)

Arguments

object
An object of class GENOME
gff.file
The corresponding GFF file
chr
The chromosome/scaffold identifier
attribute
The attribute to use for splitting

Value

  • The returned value is an object of class "GENOME" See GENOME.class.split@region.names and GENOME.class.split@region.names after splitting the data.

Details

The algorithm splits the data into attributes. An attribute can be "gene_name", "Parent" or just a single gene name like "geneXYZ".

Examples

Run this code
# GENOME.class <- readVCF("chr1.vcf.gz",1000,"1",1,100000)
# GENOME.class.split <- split_data_into_GFF_attributes(GENOME.class,"Homo_sapiens.GRCh37.73.gtf", 
# "1", "gene_name")
# GENOME.class.split@region.names
# GENOME.class.split@feature.names

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