"FilterResults"(run=Rolexa.env,results)
FilterResults(run,...)
SeqScore
FilterResults
returns an object suitable for
SaveResults
FilterResults
filters the sequences according to the
entropy thresholds set by
IThresholds
and applies the
tag length cutoff
MinimumTagLength
. The algorithm works as follows: for each tag the base entropies are
searched for a sub-vector k+1:l
such that
sum(entropy[n,5+k+1:l])<=IThresholds[l]=
where l=MinimumTagLength
. If
such a sub-vector exists, it is then extended in both direction until the
total entropy exceeds the threshold:
sum(results[n,5+k1:k2])>IThresholds[k2-k1+1]
.
The tag is then shortened: substr(results[n,5],k1,k2)
, but [ACGT]
bases to left of k1
and to the right of k2
are
added. The Barcode
first bases of the tags
will always be included in a separate column if this parameter has
been set. If PET=TRUE
then the whole
procedure is applied independently to each half of the sequence (and
two separate sets of tags and scores are returned) and
the barcode (if any) is assumed to be in-between the two paired tags.
SeqScore
and FilterResults
to
produce results for SaveResults