is.valid.seq: verifies that sequences are correct given coordinates and a...

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

verifies that sequences are correct given coordinates and a reference

Description

verifies that sequences are correct given coordinates and a reference

Usage

is.valid.seq(
	x,
	querySeq,
	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
querySeq	a vector of sequences the same length as x
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 querySeq

Author(s)

Daryl Waggott, Syed Haider

Examples

if (check.binary("bedtools")) {
  index <- get.example.regions();
  a <- index[[1]];
  a <- get.fasta(bedr.sort.region(a));
  is.valid.seq(x = a, querySeq = a$sequence);
}

bedr documentation built on April 11, 2025, 5:52 p.m.