[Bioc-sig-seq] srFilter function in ShortRead

[Vincent Carey]

there are undoubtedly many possibilities, here is a simple stepwise approach
using a closure to satisfy the constraint on filter form (must be
function of one argument 'x')

firstIsX = function(sro, X) {
 as(substr(sread(sro),1,1),"character") == X
}

firstIsA = srFilter(function(x) firstIsX(x,"A"), name="firstIsA")

example(srFilter) # to get aln, an instance of AlignedRead, into scope

aln[firstIsA(aln)]  # seems to comply

sread( aln[ firstIsA(aln) ] )  # seems to do what was requested


On Tue, Feb 9, 2010 at 3:30 PM, joseph <jdsandjd at yahoo.com> wrote:
> Hi
> can you help me create a filter to subset only reads that start with a particular nucleotide, for example G?
> Many thanks
> -Joseph
>
>
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