segmentOverlaps_bed | R Documentation |
This function produces the same output as segmentOverlaps
,
but using a command-line call to UCSC bedtools, which must be
installed, and starting from normal genome coordinates (w/o indexing;
0-based and inclusive start and end). It temporarily creates bed files,
and can require quite a lot of disk space. However, it is faster
than segmentOverlaps
, and likely better tested.
segmentOverlaps_bed(
query,
target,
qclass,
tclass,
prefix = "cl_",
chrL,
perm,
tmpdir,
runid,
overlaps = FALSE,
symmetric = FALSE,
save.permutations = FALSE,
verb = 1
)
query |
query segment table, will be permutated. |
target |
target segment table. |
qclass |
column name which holds a sub-classification (clustering) of the query segments, omit to use all. |
tclass |
column name which holds a sub-classification (clustering) of the target segments, omit to use all. |
prefix |
prefix to be added to the name and score columns of bed files (column 4,5), used to get unique names. |
chrL |
obligatory vector of chromosome length, in the order
used as index in the |
perm |
number of permutations for calculating statistics. |
tmpdir |
temporary directory, useful to provide for debugging, or exploring detailed results. |
runid |
use this ID for the run, for more recognizable jobnames. This is potentially dangerous since each call MUST have a unique name. |
overlaps |
allow overlaps in the permutations of query segments. |
symmetric |
treat test as symmetric. This is only useful for the case where overlaps all segments from the forward strand and the reverse strand are tested, to find antisense overlaps within a segment classification. |
save.permutations |
save permutated query bed files used
in p-value calculation. If this is provided together with
|
verb |
verbosity level, 0: silent. |
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