I have a file comprised of with multiple (thousands) of single-molecule reads, and a score for multiple k-mers in each of these reads.

chr start end read score

1 500 505 read1 5

1 5010 515 read1 8

1 501 506 read2 2

1 520 525 read2 -3

I would like to make a heatmap where each read is a row and the position along the chromosome is the column. I've imported it into a GRange object, and can easily split it by read-name in a loop, but is there an easy way to make a heatmap or a matrix from it? All the reads cover different (sometimes overlapping) parts of the same genomic region.

Thanks

Danny

You should probably use Gviz for that. See the vignette and help page for DataTrack.