bedr.merge.region {bedr} | R Documentation |
merge i.e. collapse overlpaping regions
Description
merge i.e. collapse overlpaping regions
Usage
bedr.merge.region(
x,
distance = 0,
list.names = TRUE,
number = FALSE,
stratify.by = NULL,
check.zero.based = TRUE,
check.chr = TRUE,
check.valid = TRUE,
check.sort = TRUE,
verbose = TRUE
);
Arguments
x |
input |
distance |
maximum distance between regions to be merged. defaults to 0 which means overlapping or bookended features. note that you can use negative distances to enforce a minimum overlap. |
list.names |
output list of names for merged items |
number |
output number of merged items |
stratify.by |
a column name indicating the groups to stratify merging within i.e. gene name. merging will not happen between groups. |
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 the sort order be checked |
verbose |
should log messages and checking take place |
Author(s)
Daryl Waggott
References
http://bedtools.readthedocs.org/en/latest/content/tools/merge.html
Examples
if (check.binary("bedtools")) {
index <- get.example.regions();
a <- index[[1]];
a.sort <- bedr.sort.region(a);
a.merged <- bedr.merge.region(a.sort);
}
[Package bedr version 1.0.7 Index]