Example of GenomicRanges's tileGenome, which I think demonstrates its power. This might be a bit faster as a custom script in Python or C, but (1) this would take longer and (2) this is much more interactive (3) on real data, it's actually pretty fast. Stuff like this is why Bioconductor should be in every bioinformatician's toolkit.

summarizeByTile.R

library(GenomicRanges)

summarizeByTile <-
# given a GRanges (or some sort of ranged data) object `x`, and a
# *corresponding* vector values to summarize `y` (these *must*
# correspond), calculate the summary per tile with the function `fun`.
# Note: this is still beta; wider tests coming, use with caution.
function(x, y, tiles, fun, mcol_name="y") {
    stopifnot(length(x) == length(y))

    if (is(tiles, "GRangesList"))
        tiles <- unlist(tiles)

    # find overlaps between ranges object x and tiles
    hits <- findOverlaps(x, tiles)
    message(sprintf("summarizeByTile: %d overlaps found between x (%d rows) and genome tiles (%d rows)",
                    length(hits), length(x), length(tiles)))

    # split y by hits in tiles
    split_y <- split(y[queryHits(hits)], subjectHits(hits))

    if (!is.null(mcol_name)) {
        tile_summaries <- tiles[unique(subjectHits(hits))]
        mcols(tile_summaries)[mcol_name] <- sapply(split_y, fun)
        return(tile_summaries)
    } else
        sapply(split_y, fun)
}

# toy example
chr1_length <- c(chr1=1000)
tiles <- tileGenome(chr1_length, tilewidth=100)
snps <- GRanges("chr1", IRanges(sample(seq_len(chr1_length)), width=1), genotype=sample(c("0/0", "0/1", "1/1"), chr1_length, replace=TRUE))

tile_hets <- summarizeByTile(snps, mcols(snps)$genotype, tiles, fun=function(x) sum("0/1" == x)/length(x))

## > tile_hets
## > summarizeByTile(snps, mcols(snps)$genotype, tiles, fun=function(x) sum("0/1" == x)/length(x))
## summarizeByTile: 1000 overlaps found between x (1000 rows) and genome tiles (10 rows)
## GRanges with 10 ranges and 1 metadata column:
##            seqnames      ranges strand |         y
##               <Rle>   <IRanges>  <Rle> | <numeric>
##        [1]     chr1 [101,  200]      * |      0.31
##        [2]     chr1 [801,  900]      * |      0.31
##        [3]     chr1 [901, 1000]      * |      0.43
##        [4]     chr1 [401,  500]      * |       0.3
##        [5]     chr1 [601,  700]      * |      0.42
##        [6]     chr1 [701,  800]      * |      0.31
##        [7]     chr1 [201,  300]      * |      0.28
##        [8]     chr1 [501,  600]      * |      0.34
##        [9]     chr1 [301,  400]      * |      0.28
##       [10]     chr1 [  1,  100]      * |      0.35
##       ---
##       seqlengths:
##        chr1
##        1000