4
$\begingroup$

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?

$\endgroup$

1 Answer 1

8
$\begingroup$

The GenomicRanges package is a great place to start, something like this:

library(GenomicRanges)

# make a GenomicRanges set corresponding to the genes
genes.gr = makeGRangesFromDataFrame(df = genes, start.field = "start", end.field = "stop", seqnames.field = "chrom")

# turn your windows into a data frame and make a GenomicRanges set from that
windows = ...
windows.gr = makeGRangesFromDataFrame(df = windows ...

# find overlaps between the two sets
olaps = findOverlaps(genes.gr, windows.gr)

# output relevant fields
cat(paste(genes[queryHits(olaps),"gene_id"], windows[subjectHits(olaps),"window_id"]))
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.