Creates pairs of coordinates from indexed anchor and bait genomic coordinates according to distance constraints.
Usage
SearchPairs(
indexAnchor.gnr = NULL,
indexBait.gnr = NULL,
minDist.num = NULL,
maxDist.num = NULL,
verbose.bln = FALSE,
cores.num = 1
)Arguments
- indexAnchor.gnr
<GRanges>: A first indexed GRanges object used as pairs anchor (must be indexed using IndexFeatures()).
- indexBait.gnr
<GRanges>: A second indexed GRanges object used as pairs bait (must be indexed using IndexFeatures()). If NULL, indexAnchor.gnr is used instead (Default NULL)
- minDist.num
<numeric>: Minimal distance between anchors and baits. (Default NULL)
- maxDist.num
<numeric>: Maximal distance between anchors and baits. (Default NULL)
- verbose.bln
<logical>: If TRUE show the progression in console. (Default FALSE)
- cores.num
<integer> : Number of cores to use. (Default 1)
Examples
# Data
data(Beaf32_Peaks.gnr)
# Index Beaf32
Beaf32_Index.gnr <- IndexFeatures(
gRange.gnr_lst = list(Beaf = Beaf32_Peaks.gnr),
chromSize.dtf = data.frame(seqnames = c("2L", "2R"), seqlengths = c(23513712, 25286936)),
binSize.num = 100000
)
# Beaf32 <-> Beaf32 Pairing
Beaf_Beaf.gni <- SearchPairs(indexAnchor.gnr = Beaf32_Index.gnr)