fastseg - a fast segmentation algorithm
Description
fastseg implements a very fast and efficient segmentation
algorithm. It has similar functionality as DNACopy (Olshen and
Venkatraman 2004), but is considerably faster and more
flexible. fastseg can segment data from DNA microarrays and
data from next generation sequencing for example to detect copy
number segments. Further it can segment data from RNA
microarrays like tiling arrays to identify transcripts. Most
generally, it can segment data given as a matrix or as a
vector. Various data formats can be used as input to fastseg
like expression set objects for microarrays or GRanges for
sequencing data. The segmentation criterion of fastseg is based
on a statistical test in a Bayesian framework, namely the cyber
t-test (Baldi 2001). The speed-up arises from the facts, that
sampling is not necessary in for fastseg and that a dynamic
programming approach is used for calculation of the segments'
first and higher order moments.