How can I prune these column ranges given another file in R?

Question

I have a data.frame1 like:

1    bin chrom chromStart  chromEnd    name score
2     12  chr1   29123222  29454711 -5.7648   599
3    116  chr1   45799118  459         


        

Answer 1

+1 for suggesting IRanges::findOverlaps.

Here's a solution using findOverlaps and GenomicRanges:

library(GenomicRanges);

df1 <- cbind.data.frame(
    bin = c(12, 116, 117, 121, 133, 147),
    chrom = c("chr1", "chr1", "chr1", "chr1", "chr1", "chr1"),
    chromStart = c(29123222, 45799118, 46327104, 50780759, 63634657, 77825305),
    chromEnd = c(29454711, 45986770, 46490961, 51008404, 63864734, 78062178),
    name = c(-5.7648, -4.8403, -5.3036, -4.4165, -4.8096, -5.4671),
    score = c(599, 473, 536, 415, 469, 559));

df2 <- cbind.data.frame(
    chrom = c("chr1", "chr1", "chr1", "chr1", "chr1"),
    chromStart = c(63600000, 45800000, 29100000, 50400000, 46500000),
    chromEnd = c(63700000, 45900000, 29400000, 50500000, 46600000),
    N = c(1566, 1566, 1566, 1566, 1566));

# Make GRanges objects from dataframes
gr1 <- with(df1, GRanges(
    chrom, 
    IRanges(start = chromStart, end = chromEnd), 
    bin = bin, 
    name = name, 
    score = score));

gr2 <- with(df2, GRanges(
    chrom,
    IRanges(start = chromStart, end = chromEnd),
    N = N));

# Get overlapping features
hits <- findOverlaps(query = gr1, subject = gr2);

# Get features from gr1 that overlap with features from gr2
idx1 <- queryHits(hits);
idx2 <- subjectHits(hits);
gr <- gr1[idx1];

# Make sure that we only keep the intersecting ranges
start(gr) <- ifelse(start(gr) >= start(gr2[idx2]), start(gr), start(gr2[idx2]));
end(gr) <- ifelse(end(gr) <= end(gr2[idx2]), end(gr), end(gr2[idx2]));

print(gr);

GRanges object with 3 ranges and 3 metadata columns:
      seqnames               ranges strand |       bin      name     score
         <Rle>            <IRanges>  <Rle> | <numeric> <numeric> <numeric>
  [1]     chr1 [29123222, 29400000]      * |        12   -5.7648       599
  [2]     chr1 [45800000, 45900000]      * |       116   -4.8403       473
  [3]     chr1 [63634657, 63700000]      * |       133   -4.8096       469
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

# Turn GRanges into a dataframe
df <- data.frame(bin = mcols(gr)$bin, 
                 chrom = seqnames(gr), 
                 chromStart = start(gr), 
                 chromEnd = end(gr), 
                 name = mcols(gr)$name, 
                 score = mcols(gr)$score);
print(df);