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")