process.input: process.input

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

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

Author(s)

Daryl Waggott

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)

}

Example output

######################
#### bedr v1.0.7 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... FAIL

bedr documentation built on May 2, 2019, 11:36 a.m.