How can I find the overlapping values of these ranges in R?

Question

I have a df1 called ranges like:

1    bin chrom chromStart  chromEnd    name score
2     12  chr1   836780    856723    -5.7648   599
3    116  chr1   1693001   1739032   -4.8403   473
4    117  chr1   1750780   1880930   -5.3036   536
5    121  chr1   2020123   2108890   -4.4165   415

I also have a data.frame called viable like:

   chrom   chromStart  chromEnd        N
chr1      840000       890000       1566
chr1      1690000      1740000      1566
chr1      1700000      1750000      1566
chr1      1710000      1760000      1566
chr1      1720000      1770000      1566
chr1      1730000      1780000      1566
chr1      1740000      1790000      1566
chr1      1750000      1800000      1566
chr1      1760000      1810000      1566

Basically I have ranges of values from chromStart to chromEnd in ranges. I also have a list of ranges in the df2 viable. The ranges in viable are much smaller. I want to test the ranges from ranges and make sure that the full range falls within ranges that are viable. How can I do this?

The output I want is a data.frame like:

1    bin chrom chromStart  chromEnd    name score
2     12  chr1   840000    856723    -5.7648   599
3    116  chr1   1693001   1739032   -4.8403   473
6    133  chr1   1750780   1880930   -4.8096   469

Why the double-posting? The answer is given [here](http://stackoverflow.com/a/39844131/6530970). Different numbers don't make it a different question. — Maurits Evers, Oct 06 '16 at 06:54

score 2 · Accepted Answer · answered Oct 06 '16 at 06:32

You could try using the GenomicRanges package.

library(dplyr)
library(GenomicRanges)

Here we load in the the example input data. (This is an inelegant way to do this -- I know... but I was lazy and the sublime multiline edit made it easy.) Note: I don't know where the "1" column means, but I kept it in the data.

ranges <-
  rbind(
    c("2","12","chr1","836780","856723","-5.7648","599"),
    c("3","116","chr1","1693001","1739032","-4.8403","473"),
    c("4","117","chr1","1750780","1880930","-5.3036","536"),
    c("5","121","chr1","2020123","2108890","-4.4165","415")
  ) %>% 
  as.data.frame()
colnames(ranges) <-
  c("1","bin","chrom","chromStart","chromEnd","name","score")

viable <-
  rbind(
    c("chr1","840000","890000","1566"),
    c("chr1","1690000","1740000","1566"),
    c("chr1","1700000","1750000","1566"),
    c("chr1","1710000","1760000","1566"),
    c("chr1","1720000","1770000","1566"),
    c("chr1","1730000","1780000","1566"),
    c("chr1","1740000","1790000","1566"),
    c("chr1","1750000","1800000","1566"),
    c("chr1","1760000","1810000","1566")
  ) %>%
  as.data.frame()
colnames(viable) <-
  c("chrom","chromStart","chromEnd","N")

## Need columns to be integers
ranges <-
  ranges %>%
  tbl_df() %>%
  mutate(
    chromStart = chromStart %>% as.character %>% as.integer,
    chromEnd = chromEnd %>% as.character %>% as.integer
    )
viable <-
  viable %>%
  tbl_df() %>%
  mutate(
    chromStart = chromStart %>% as.character %>% as.integer,
    chromEnd = chromEnd %>% as.character %>% as.integer
    )

Here is where my answer begins:

Reformat dataframe to GenomicRanges class
Find the regions by doing an intersection
Add in the bin, name, and score columns using the findOverlaps. (Note, this information is removed during the intersection because there is not necessarily a 1:1 mapping)
Reformat output back into a dataframe

Done

gr.ranges <-
  makeGRangesFromDataFrame(ranges,
                           keep.extra.columns = T,
                           seqnames.field = "chrom",
                           start.field = "chromStart",
                           end.field = "chromEnd")
gr.viable <-
  makeGRangesFromDataFrame(viable,
                           keep.extra.columns = T,
                           seqnames.field = "chrom",
                           start.field = "chromStart",
                           end.field = "chromEnd")

# To find the intersects
gr.intersect <-
  GenomicRanges::intersect(gr.ranges, gr.viable)

# For linking up the non- chrom,start,end columns
gr.hits <-
  GenomicRanges::findOverlaps(gr.intersect, gr.ranges)

output <-
  gr.intersect[queryHits(gr.hits)]
mcols(output) <-
  mcols(gr.ranges[subjectHits(gr.hits)])
output

# Reformat to dataframe
output %>%
  as.data.frame() %>%
  select(`1` = X1, bin, chrom = seqnames, chromStart = start, chromEnd = end, name, score)

How can I find the overlapping values of these ranges in R?

1 Answers1

Here is where my answer begins:

Linked