R_functions

a set of useful R functions for genomic analysis

checkDivergent Function

An R function for checking whether loci are divergent in a set of strains. script

Notes

This function uses GenomicRange and IRanges packages to look for intersections between user provided loci and the Andersen Lab divegent_regions_strain.bed file. Users can also specify which strains they would like to search within. Loci are passed in the form of a range III:999124-999168.

# set parameters
strains <- c("JU310", "MY2693")
loci <- c("III:999129-999250", "II:999129-999250", "I:1208020-1208021", "I:1208024-1208025")
bedPath <- "data/divergent_regions_strain.bed"

# example usage
checkDivergent(strains = strains, loci = loci, bedPath = bedPath)
   chrom   start     end             locus strain divergent
1:     I 1208020 1208021 I:1208020-1208021  JU310      TRUE
2:     I 1208024 1208025 I:1208024-1208025  JU310      TRUE
3:     I 1208020 1208021 I:1208020-1208021 MY2693      TRUE
4:     I 1208024 1208025 I:1208024-1208025 MY2693      TRUE