is.valid.ref: verifies the reference sequence in a vcf

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

Description

verifies the reference sequence in a vcf

Usage

is.valid.ref(
	x,
	fasta = NULL,
	strand = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	input bed object
fasta	a reference build in fasta format
strand	should strand be used. if reverse then the sequence will be reverse complemented
check.zero.based	should 0 based coordinates be checked
check.chr	should chr prefix be checked
check.valid	should the region be checkded for integerity
check.sort	should regions be checked for sort order
check.merge	should overlapping regions be checked
verbose	should log messages and checking take place

Value

a logical vector the length of the input

Author(s)

Daryl Waggott

Examples

vcf.path <- system.file("extdata/callerA.vcf.gz", package = "bedr");
vcf.data <- read.vcf(vcf.path, split.info = TRUE);
vcf.data$vcf <- vcf.data$vcf[, 
	c("CHROM", "POS", "END", setdiff(colnames(vcf.data$vcf), c("CHROM", "POS", "END")))
	];
vcf.data$vcf$CHROM <- paste("chr", vcf.data$vcf$CHROM, sep = "");

## Not run: 
	# need reference sequence FASTA and index file to run this, as 'fasta' parameter
	is.valid.ref(vcf.data);
	
## End(Not run)

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