I am trying to run some frequency based stats to identify selective sweep in my study system using Rpackage "PopGenome".
To proceed with it I have split my genome data (whole genome sequencing) into 5MB chunks
cregions <- character(31)
cregions[1] <- "1-5000000"
cregions[2] <- "5000001-10000000"
cregions[3] <- "10000001-15000000"
cregions[4] <- "15000001-20000000"
cregions[5] <- "20000001-25000000"
cregions[6] <- "25000001-30000000"
cregions[7] <- "30000001-35000000"
....
I have a bunch of genes and I want to know each of my genes falls within the range of which intervals in the above list.
these are my genes:
chrom start stop gene_id
Chr01 107310787 107323633 gene2748
Chr01 113789595 113794851 gene2894
Chr01 159041389 159068535 gene4806
Chr02 2742629 2758060 gene4846
I'd like to get an out put like this
gene2748 window_2
gene2894 window_3
...
Any idea how I can do it in R?