segmentOverlaps | R Documentation |
calculates the Jaccard index, including a simple permutation test, between
different classes in a query and a target set of segments
(genomic intervals), where coordinates have been converted to a
continuous index over all chromosomes with coor2index
.
Note, that this ignores chromosome borders!
segmentOverlaps(
query,
target,
qclass,
tclass,
total,
perm = 0,
symmetric = FALSE,
verb = 1
)
query |
query set of segments |
target |
target set of segments |
qclass |
column name which holds a sub-classification (clustering) of the query segments, omit or pass empty string ("") to use all |
tclass |
column name which holds a sub-classification (clustering) of the target segments, omit or pass empty string ("") to use all |
total |
total length of the query range (genome length), if missing the start of the first segment is also used as end |
perm |
number of permutations to perform |
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. |
verb |
integer level of verbosity, 0: no messages, 1: show messages |
Reports the Jaccard index (J=intersect/union)
) between
two distinct sets of segments (matrix "jaccard" in the results object),
and the relative intersect lengths, i.e., intersect divided by
the total target length (matrix "intersect.target") or the total
query length (matrix "intersect.query").
If argument perm>0
, a simple permutation is performed,
sampling randomly from
all inter-segment distances and segment lengths, and ignoring optional
query sub-classifications (argument qclass
). Note, that chromosome
ends are ignored. The total length of the query range (genome length, for
both strands, if both are used) can be passed in argument total
,
and if missing the start of the first segment is also used as the distance
of the final segment to the query range end.
The results of the permutation test (argument perm>0
) can be
plotted directly with plotOverlaps
, where option text
allows to plot either the jaccard index or the relative intersect sizes.
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