split_data_into_GFF_attributes: Split the data into GFF attributes

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

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

Details

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

Value

The returned value is an object of class "GENOME"
See [e-mail] and [e-mail]
after splitting the data.

Examples

# 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")
# [e-mail]
# [e-mail]

Example output

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/work/tmp/tmp/RtmphX06Ue"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.