bedr (version 1.0.0)

process.input: process.input

Description

process.input

Usage

process.input(
	input, 
	tmpDir = NULL,
	include.names = TRUE, 
	check.zero.based = TRUE, 
	check.chr = TRUE, 
	check.valid = TRUE, 
	check.sort = TRUE, 
	check.merge = TRUE, 
	verbose = TRUE
	)

Arguments

input

regions input or a file in one of the standard formats. these are bed, vcf, gff, bam, sam, csv, tsv, txt

tmpDir

The directory to be used for writing files

include.names

should the names of the input files be included in the output

check.zero.based

should 0 based coordinates be checked

check.chr

should chr prefix be checked

check.valid

should the region be checked for integerity

check.sort

should the region sorting be checked

check.merge

should overlapping regions be checked

verbose

messages and checks

Value

• list of input files

Examples

if (check.binary("bedtools")) {

index <- get.example.regions();
a <- index[[1]];
a <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
a.processed <- process.input(a, verbose = FALSE)

}