View source: R/bedr.join.multiple.region.R
bedr.join.multiple.region | R Documentation |
join multiple objects
bedr.join.multiple.region(
x = list(),
fraction.overlap = 1/1e9,
empty = FALSE,
missing.values = ".",
cluster = FALSE,
species = "human",
build = "hg19",
check.zero.based = TRUE,
check.chr = TRUE,
check.valid = TRUE,
check.sort = TRUE,
check.merge = TRUE,
verbose = TRUE
)
x |
list of region objects |
fraction.overlap |
proportion of bases to be considered an overlap |
empty |
print rows if no match |
missing.values |
missing value character |
cluster |
TRUE/FALSE for clustering |
species |
species i.e. human or mouse |
build |
genome build to use for empty regions |
check.zero.based |
should 0 based coordinates be checked |
check.chr |
should chr prefix be checked |
check.valid |
check if region is valid |
check.sort |
check if region is sorted |
check.merge |
check if overlapping regions are merged |
verbose |
messages and checks |
Daryl Waggott
http://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html
if (check.binary("bedtools")) {
index <- get.example.regions();
a <- index[[1]];
b <- index[[2]];
a.sort <- bedr.sort.region(a);
b.sort <- bedr.sort.region(b);
d <- get.random.regions(100, chr="chr1", sort = TRUE);
a.mult <- bedr.join.multiple.region(x = list(a.sort,b.sort,bedr.sort.region(d)));
}
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