getSIFromND: getSIFromND - calculating splicing index of two coverages
In rnaSeqMap: rnaSeq secondary analyses

Description Usage Arguments Value Author(s) Examples

This function calculates the splicing index value of two sample coverages from a NucleotideDistr object. It is assumed that the region in the NucleotideDistr is a single gene. Splicing index is calculated in similar way to the implementation for exon Affy microarrays (see Gardina et al, Genome Biology, 2007 for details), but it is run for each nucleotide in the region and instead of gene-level average expression values, it uses sums of reads for both samples.

1	getSIFromND(nd, exps)

`nd`	`NucleotideDistr` object with coverages
`exps`	a pair of numbers of samples in the experiment

NucleotideDistr object of type "FC" with a single vector of splicing index values

Michal Okoniewski, Anna Lesniewska

#  if (xmapConnected())  
#  {
#    rs <- newSeqReads(1,1,20000,1)
#    nd.cov <- getCoverageFromRS(rs,1:3)
#    nd.fc <- getSIFromND(nd.cov,c(1,3))
#  }