Subsetting a data by a regions from BED file

Question

[zizigolu]

Hello

I have a big data like

> head(r@data)
   Tumor_Sample_Barcode Chromosome Start_Position End_Position Reference_Allele
1:    LP6005334-DNA_H01       chr1       89616151     89616151                -
2:    LP6005334-DNA_H01       chr6       51909815     51909815                A
3:    LP6005334-DNA_H01      chr16       20556547     20556547                -
4:    LP6005334-DNA_H01      chr17       66992092     66992092                -
5:    LP6005334-DNA_H01      chr20       13251339     13251339                -
6:    LP6005334-DNA_H01      chr20       35929770     35929771

> dim(r@data)
[1] 6461  141
>

I also have a bed file like

1   11866   12229
1   12610   12723
1   13218   14411
1   30363   30505
1   34551   35176

How I can subset my first data to this BED regions in R?

[zx8754]

Search for "merge by range overlap", related SO post: https://stackoverflow.com/q/24480031/680068

And see my example answer here: A: Subsetting large list of SNPs with R

[zizigolu]

Thank you so much

I used your example answer without error