| calculateDistances {GenomicInteractions} | R Documentation |
This function takes a GInteractions object and calculates the distances
between the anchors according to the value of method. The distances returned
follow the same convention as distance(x, y) in GenomicRanges where the
distance between adjacent regions is 0. Note that if anchors are overlapping
this method will print a warning and return the distance as 0.
calculateDistances(GIObject, method = "midpoint", floor = TRUE) ## S4 method for signature 'GInteractions' calculateDistances(GIObject, method = "midpoint", floor = TRUE)
GIObject |
A GInteractions object |
method |
Character vector indicating how to calculate distances, must be one of ‘midpoint’, ‘outer’, ‘inner’. |
floor |
A logical specifying whether to round down distances to nearest base pair or not. Default TRUE. |
An vector containing the distances between anchors/GRanges, NA if on different chromosomes, rounded down to the nearest bp.
library(GenomicRanges)
anchor.one = GRanges(c("chr1", "chr1", "chr1", "chr1"), IRanges(c(10, 20, 30, 20), width=5))
anchor.two = GRanges(c("chr1", "chr1", "chr1", "chr2"), IRanges(c(100, 200, 300, 50), width=5))
interaction_counts = sample(1:10, 4)
test <- GenomicInteractions(anchor.one, anchor.two, experiment_name="test",
description="this is a test", counts=interaction_counts)
calculateDistances(test, method="midpoint")