bedr.sort.region {bedr} | R Documentation |
sort a region file
Description
sort a region file
Usage
bedr.sort.region(
x,
method = "lexicographical",
engine = "R",
chr.to.num = c("X" = 23, "Y" = 24, "M" = 25),
check.zero.based = TRUE,
check.chr = TRUE,
check.valid = TRUE,
check.merge = TRUE,
verbose = TRUE
)
Arguments
x |
a region object or index |
method |
natural or lexicographic |
engine |
what analytical engine to use for sorting i.e. bedtools, bedops, gnu unix |
chr.to.num |
chromosome letter names to numbers map. Defaults to Homo sapiens i.e c("X" = 23, "Y" = 24, "M" = 25) |
check.zero.based |
should 0 based coordinates be checked |
check.chr |
should chr prefix be checked |
check.valid |
should the region be checked for integerity |
check.merge |
should overlapping regions be checked |
verbose |
should log messages and checking take place |
Author(s)
Daryl Waggott
References
http://bedtools.readthedocs.org/en/latest/content/tools/sort.html
Examples
if (check.binary("bedtools")) {
index <- get.example.regions();
a <- index[[1]];
b <- bedr.sort.region(a);
}
[Package bedr version 1.0.7 Index]