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Find signal intensity of intergenic regions.

Source: R/general_bioinfo.R
get_intergenic_signals.Rd

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

if (FALSE) {
#' 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 = "")))
}