splicing.index {exonmap}R Documentation

Find probesets involved in differential splicing for two treatments

Description

Reads expression data and using its pData, calculates splicing index for each probeset in exons of genes from the list. The splicing index formula come from the Affy white paper "Alternative Transcript Analysis Methods for Exon Arrays".

Usage

splicing.index(x, genes, group, members, median.gene=TRUE, vector.out=TRUE, by.chip=FALSE)

Arguments

x eSet for which splicing is to be calculated
genes Vector of Ensembl gene names to check
group Group name from covdesc
members Two treatments to be chosen from the group
median.gene If FALSE, mean of exon probeset values is used for gene-level summary, instead of median.
vector.out Vector or tabular output
by.chip Type of the algorithm - gene average by chip, as in Affymetrix paper or by group members

Details

Splicing index operates on expression values of probesets normalized with gene-level expression. The value of the index may have values from -1 to 1.

Value

A vector of values of splicing index for each probeset - the further from 0, the more significant the splicing. Or a table with names of genes, exon, probesets, expression and splicing index. In the case of "by chip" algorithm, the results include si and pval slots with values of splicing index and p-values of t-test between group members.

Author(s)

Michal J Okoniewski

References

http://bioinformatics.picr.man.ac.uk/

See Also

splanova, pData

Examples

 
  ## Not run: 
    gg <- probeset.to.gene(c("2326780","2326822" ))
    spl.idx <-  splicing.index(x.rma, gg, "group", c("a","b"))
  
## End(Not run)

[Package exonmap version 1.4.3 Index]