Creates pairs from genomic index. — SearchPairs • HicAggR

Creates pairs of coordinates from indexed anchor and bait genomic coordinates according to distance constraints.

Usage

SearchPairs(
  indexAnchor = NULL,
  indexBait = NULL,
  minDist = NULL,
  maxDist = NULL,
  exclude_duplicates = TRUE,
  exclude_self_interactions = TRUE,
  verbose = FALSE,
  cores = 1
)

Arguments

indexAnchor: : A first indexed GRanges object used as pairs anchor (must be indexed using IndexFeatures()).
indexBait: : A second indexed GRanges object used as pairs bait (must be indexed using IndexFeatures()). If NULL, indexAnchor is used instead (Default NULL)
minDist: : Minimal distance between anchors and baits. (Default NULL)
maxDist: : Maximal distance between anchors and baits. (Default NULL)
exclude_duplicates: Should duplicated pairs ("2L:100_2L:150" & "2L:150_2L:100") be removed? (Default: TRUE)
exclude_self_interactions: Should pairs between the same bin ("2L:100_2L:100") be excluded? (Default: TRUE)
verbose: : Show the progression in console? (Default FALSE)
cores: : Number of cores to use. (Default 1)

Value

A GInteractions object.

Details

SearchPairs

Examples

# Data
data(Beaf32_Peaks.gnr)

# Index Beaf32
Beaf32_Index.gnr <- IndexFeatures(
    gRangeList = list(Beaf = Beaf32_Peaks.gnr),
    chromSizes = data.frame(seqnames = c("2L", "2R"),
        seqlengths = c(23513712, 25286936)),
    binSize = 100000
)

# Beaf32 <-> Beaf32 Pairing
Beaf_Beaf.gni <- SearchPairs(indexAnchor = Beaf32_Index.gnr)