get.feature.names: Feature informations and GFF-attributes

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

Description

Returns feature names and additional attributes for a given region

Usage

get.feature.names(object, gff.file, chr)

Arguments

object	An object of class GENOME
gff.file	The corresponding GFF file
chr	The chromosome/scaffold identifier

Details

The algorithm uses the information stored in [e-mail] to iterate
over the GFF file and returns attribute plus feature informations for each given region.
Note, the functions splitting.data, split_data_into_GFF_attributes or sliding.window.transform
should be performed prior to that.

The slot region.names must have the following form: "pos1 - pos2".

Value

The returned value is a character vector of length length([e-mail])

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]
# info <- get.feature.names(GENOME.class.split, gff.file="Homo_sapiens.GRCh37.73.gtf", chr="1")
# GENOME.class.split <- splitting.data(GENOME.class, subsites="gene")
# [e-mail]
# info <- get.feature.names(GENOME.class.split, gff.file="Homo_sapiens.GRCh37.73.gtf", chr="1")

Example output

Loading required package: ff
Loading required package: bit

Attaching package: ‘bit’

The following object is masked from ‘package:base’:

    xor

Attaching package ff
- getOption("fftempdir")=="/work/tmp/tmp/RtmpfTf4nR/ff"

- 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: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.