ucsc.pos.subset: ucsc.pos.subset
In drmjc/genomics: Genomics related functions.

Description Usage Arguments Details Value Author(s) Examples

For a set of UCSC style intervals, produce a new set of intervals that are subsets of those intervals. Strand must be provided, because intervals are strand-less, but the logic to subset an interval depends very much on the strand.

1	ucsc.pos.subset(intervals, start, stop, strand)

`intervals`	vector of UCSC style intevals, eg "chr1:100-300"
`start`	vector of numerics defining the starting base within each interval (1-based)
`stop`	vector of numerics defining the ending base within each interval (1-based). NB stop can be longer than the original interval.
`strand`	either a charcter vector of "+"/"-", or 0,1, or -1,1

eg: subset chr1:1000-1100 (+) to the interval that starts at 2-7 -> chr1:1001-1006 eg: subset chr1:1000-1100 (-) to the interval that starts at 2-7 -> chr1:1094-1099

a vector of UCSC style intervals, adjusted as detailed above

Mark Cowley, 2009-01-08

ucsc.pos.subset("chr1:1000-1100", 1,11, "+")
# [1] "chr1:1000-1010"
ucsc.pos.subset("chr1:1000-1100", 1,11, "-")
# [1] "chr1:1090-1100"
# (you can use > 1 entry too.)