Subset genomic intervals by other intervals

Question

[Filago]

Hello,

I have a bed-like dataframe in R and want to subset it by another bed-like file e.g.:

Bed file 1:

Chr Start End

1     1      10

Bed file2:

Chr Start End

1     5      13

Final bed file:

Chr Start End

1     5      10

So the final bed file should only consist of regions, which are present in both files.

Any suggestions how to do this in R?

Best,

Andreas

Answer 1

[seidel]

Use the GenomicRanges library in R. This stuff is what it's all about:

library(GenomicRanges)

a <- data.frame(Chr=1, Start=1, End=10)
b <- data.frame(Chr=1, Start=5, End=13)

# convert to GRanges objects
a <- makeGRangesFromDataFrame(a)
b <- makeGRangesFromDataFrame(b)

# get the common overlapping bits
theIntersection <- intersect(a,b)

# check your results in a genome browser
library(rtracklayer)
export(theIntersection, "intersected_features.bed")

FYI, the result:

> intersect(a,b)
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        1      5-10      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths