splanova {exonmap}R Documentation

Find probesets involved in differential splicing for multiple treatments

Description

Reads expression data and using its pData calculates F-values and finds significant cases using ANOVA. The approach is similar to MIDAS, described in Affymetrix white paper "Alternative Transcript Analysis Methods for Exon Arrays".

Usage

splanova (x,genesin, group,base, thr=0.05, probes.min=4, exonic=T, debug=0)
fval(object)
sig(object)

Arguments

x eSet for which splicing is to be calculated
genesin Vector of Ensembl gene names to check
group Group name from covdesc
base Reference treatment name for the one-way ANOVA model - must be in the group in covdesc
thr Alpha level threshold for F-test
probes.min Minimal number of probes to include the probeset in the search - see gene.to.probeset
exonic Specifies if only exonic probesets should be used - see select.probewise
debug Debug level - 0 stands for no debug messages
object a splanova object of class Splanova

Details

Value

A Splanova object with two slots : fval - list of F-values from ANOVA and sig - descriptive listing of splicing events.

Author(s)

Michal J Okoniewski

References

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

See Also

splicing.index, code{gene.to.probeset}, select.probewise, pData

Examples

 
  ## Not run: 
    gg <- probeset.to.gene(c("2326780","2326822" ))
    spl.multi <-  splanova(x.rma, gg, "group", "a", thr=0.05, debug=4)
    fval(spl.multi)
    sig(spl.multi)
  
## End(Not run)

[Package exonmap version 1.0.07 Index]