add_divergent_flag.R

library(tidyverse)
library(dplyr)
library(tidyr)
library(magrittr)
library(valr)
library(fuzzyjoin)
library(Bioconductor)

#Load Divergent Regions
divergent <- data.table::fread("~/projects/b1059/projects/Ryan/csq/flat_file/lee2020.divergent_regions_strain.bed",
                               col.names = c("chrom", "start", "end", "strain"))

#Condense Overlapping Regions (If portion of regions shared by >1 strian
condensed <- divergent %>%
  valr::bed_merge() %>%
  dplyr::mutate(DIVERGENT = "D") # Add marker to Divergent Region

#Read In Flat File
data <- data.table::fread("~/projects/b1059/projects/Ryan/csq/flat_file/WI.20210121.hard-filter.isotype.bcsq.20210401.pre.flatfile-gene-impact.tsv")


#Join the data - if a position is within a divergent region Divergent tag is added

join <- genome_join(data, condensed,  by = c(
  "CHROM" = "chrom",
  "POS" = "start",
  "POS" = "end"),
  mode = "left") %>%
  select(-chrom, -start, -end)




data.table::fwrite(join, "~/projects/b1059/projects/Ryan/csq/flat_file/WI.20210121.hard-filter.isotype.bcsq.20210401.flatfile.tsv" )