Zachary McCaw
Updated: 2022-03-02
Simple application of the GRanges package to compare two sets of loci.
devtools::install_github(repo = "zrmacc/CompareLoci")
library(CompareLoci)
# Sets of loci to compare.
left <- data.frame(
chr = c(1, 1, 1),
start = c(1, 200, 400),
end = c(100, 300, 500)
)
right <- data.frame(
chr = c(1, 1, 1, 1),
start = c(20, 50, 150, 440),
end = c(25, 75, 180, 450)
)
# Overlap statistics.
overlap_stats <- CalcOverlapStats(left, right)
show(overlap_stats)
## Loci on the left overlapping at least 1 locus on the right:
## [1] "2 of 3 (66.7%)"
##
##
## Loci on the right overlapped by at least 1 locus on the left:
## [1] "3 of 4 (75%)"
# Loci on the left overlapping at least 1 locus on the right:
show(overlap_stats@left_overlapping)
## [1] 1 3
# Loci on the right overlapping at least 1:
show(overlap_stats@right_overlapped)
## [1] 1 2 4