makeDataMethGFF {methVisual}R Documentation

GFF methylation files

Description

Create methData object from processed .gff files

Usage

makeDataMethGFF(dir,chr,start,end,meth_value)

Arguments

dir

String; The local directory where the .gff files are located

chr

String; Chromosome under study

start

Integer; The start position of genomic region under study

end

Integer; The end position of the genomic region under study

meth_value

double; level of methylation on CpG

Details

This function reads and processes GFF files and creates a list object (like the one generated by MethAlignNW()) which can be later analyzed through the visualization, classification and clustering functions.

Value

methData object

Author(s)

Arie Zackay <arie.zackay@mail.huji.ac.il>, Christine Steinhoff <steinhof@molgen.mpg.de>

Examples

methGFF <- makeDataMethGFF(dir=system.file(package="methVisual",
			"examples/GFF"),chr="7",start=0,end=70,0.75)
methGFF

[Package methVisual version 1.34.0 Index]