bedr (version 1.0.2)

tabix: Main bedtools wrapper function.

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.

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)
}