Hi,

If I have two Granges:

library(rtracklayer)
library(dplyr)
library(Granges)
gr1 <- makeGRangesFromDataFrame(
    data.frame(
        chr=rep('6',3),
        start=c(1,200,1000),
        end=c(100,300,2000),
        gene=paste0('ENSG', c('A', 'B', 'C')),
        keep.extra.columns=TRUE))

gr1
                seqnames               ranges strand | ensembl_gene_id
                   <Rle>            <IRanges>  <Rle> |     <character>
      [1]    6           [1, 100]                  * | ENSGA
      [2]    6           [200, 300]                  * | ENSGB
      [3]     6          [1000, 2000]              * | ENSGC

gr2 <- makeGRangesFromDataFrame(
    data.frame(
        chr=rep('6',3),
        start=c(70,100,1900),
        end=c(100,300,2000),
        gene=paste0('ENSG', c('A', 'B', 'C')),
        keep.extra.columns=TRUE))

gr2
                seqnames               ranges strand | ensembl_gene_id
                   <Rle>            <IRanges>  <Rle> |     <character>
      [1]    6           [70, 100]                  * | ENSGA
      [2]    6           [100, 300]                 * | ENSGB
      [3]     6          [1900, 2000]               * | ENSGC

I want to subtract gr1 to gr2 like this

gr
                seqnames               ranges strand | ensembl_gene_id
                   <Rle>            <IRanges>  <Rle> |     <character>
      [1]    6           [1, 30]                    * | ENSGA
      [3]     6          [1000, 1900]               * | ENSGC

I know some function such as findoverlap and queryHits or setdiff may can do like this, but their output is similar with bedtools subtract (may with -A also), so them may cant keep extra columns, Is there any way to keep extra columns?

Best
Zhang