get_intergenic_signals: Find signal intensity of intergenic regions.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Find signal intensity of intergenic regions.

Description

given the .gff file and .bw file function finds the intergenic regions and associate signal inensity of each region

Usage

get_intergenic_signals(bw_file, gff_file)

Arguments

bw_file	a string denoting path of .bw file
gff_file	a string denoting path of gff file.

Value

an object of class GenomicRanges::granges() which can be exported to various file formats such as bw, bed, begraph etc.

Examples

## Not run: 
#' library("magrittr")
bw_file <- system.file("extdata" ,
"example.bw" ,
package = "parcutils")
gff_file <- system.file("extdata" ,
                       "C_glabrata_CBS138_version_s02-m07-r06_features.gff" ,
package = "parcutils")
oo <- parcutils::get_intergenic_signals(bw_file = bw_file,gff_file  = gff_file)
oo %>%
    rtracklayer::export.bed(con = file(paste("intergenic", ".bed",sep = "")))
oo %>%
   rtracklayer::export.bedGraph(con = file(paste("intergenic", ".bdg",sep = "")))

## End(Not run)

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.