I am trying to extract columns based on two conditions from the indices of two overlaps. This is an example:

    df1 = data.frame(chr=c("chr1", "chr1"), start=c(20,21), stop=c(28,29), value1=c(1,2))

    df2 = data.frame(chr=c("chr1", "chr1", "chr1"), start=c(20,22, 28), stop=c(22,24,34), value2=c(3,4, 60))

    df3 = data.frame(chr=c("chr1", "chr1"), start=c(3,1), stop=c(8,4))

    df4 = data.frame(chr=c("chr1", "chr1", "chr2"), start=c(10,1, 1), stop=c(12,2, 2))

    df1_all = cbind.data.frame(df1, df3)

df2_all = cbind.data.frame(df2, df4)

Which looks like this:

    > df1_all

       chr start stop value1  chr start stop 

    1 chr1    20   28      1 chr1     3    8      

    2 chr1    21   29      2 chr1     1    4      

    > df2_all

       chr start stop value2  chr start stop 

    1 chr1    20   22      3 chr1    10   12      

    2 chr1    22   24      4 chr1     1    2      

    3 chr1    28   34     60 chr2     1    2    

I would like to get the values from data frame df1_all, 

together with the matching column from df2_all called "value2", but only for values for which both df1 overlaps df3, and df2 overlaps df4, so in this case it would be:

     chr start stop value1  chr start stop value1 value2

    chr1    21   29      2 chr1     1    4      2      4

I am almost there but I am still getting something wrong in my real data and I cannot find the bug, I have been trying to find a solution for long now so I am coming here for help and a set of new eyes on this problem. Can you please help?

This is what I have:

    df1.gr makeGRangesFromDataFrame(df1)

    df2.gr makeGRangesFromDataFrame(df2)

    df3.gr makeGRangesFromDataFrame(df3)

    df4.gr makeGRangesFromDataFrame(df4)

    # First overlap

    hits1 <- findOverlapsdf1.gr, df2.gr, maxgap = 0)

    values1 <- rep(FALSE, nrow(df2_all))

    values1[unique(subjectHits(hits1))] <- TRUE

    OBJ= data.frame(df1_all[unique(queryHits(hits1)),],

    matched.df2 = df2_all[unique(queryHits(hits1)),"value2"])

    # Second overlap

    hits2 <- findOverlapsdf3.gr, df4.gr, maxgap = 0)

    values2 <- rep(FALSE, nrow(df2_all))

    values2[unique(subjectHits(hits2))] <- TRUE

    ov = values1 & values2

    OBJ = OBJ[ov,]