tabix: Main bedtools wrapper function.

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

Description

Main bedtools wrapper function.

Usage

tabix(
	region,
	file.name,
	params = NULL,
	tmpDir = NULL,
	deleteTmpDir = TRUE,
	outputDir = NULL,
	outputFile = NULL,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

region	The regions to query the tabix'd file
file.name	The name of the bzipped/indexed tabix file to query
params	A string that includes all the extra parameters and arguments to the bedtools commmand. For example if you wanted to do a left outer join you would specificy method as intersect and use params = c("-loj -header"). If you leave input and method as defaults then this is this string represents the full command.
tmpDir	The directory to be used for writing files
deleteTmpDir	Should tmp files be deleted. helpful for diagnostics.
outputDir	The output directory. Only used if outputFile is specified. It defaults to the current working directory.
outputFile	The name of the output file. If this is specified the output will be sent to a file not an R object
check.chr	check for chr prefix
check.zero.based	check for zero based coordinates
check.valid	do all region integrity checks
check.sort	check if region is sorted
check.merge	check if region is merged
verbose	Should messages be printed to screen.

Value

The output of command with some parsing to keep it consistent with the input.

Author(s)

Daryl Waggott

See Also

genomicRanges

Examples

if (check.binary("tabix")) {
query.regions <- c("1:1000-100000", "1:1000000-1100000")
cosmic.vcf.example <- system.file(
	"extdata/CosmicCodingMuts_v66_20130725_ex.vcf.gz",
	package = "bedr"
	)
cosmic.query <- tabix(query.regions, cosmic.vcf.example, check.chr = FALSE)
}

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