is.valid.seq {bedr} | R Documentation |
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);
}
[Package bedr version 1.0.7 Index]