splanova {exonmap} | R Documentation |
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".
splanova (x,genesin, group,base, thr=0.05, probes.min=4, exonic=T, debug=0) fval(object) sig(object)
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 |
A Splanova object with two slots : fval - list of F-values from ANOVA and sig - descriptive listing of splicing events.
Michal J Okoniewski
http://bioinformatics.picr.man.ac.uk/
splicing.index
, code{gene.to.probeset}, select.probewise
, pData
## 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)