splicing.index {exonmap} | R Documentation |
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".
splicing.index(x, genes, group, members, vector.out=T, debug=0)
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 |
vector.out |
Vector or tabular output |
debug |
Debug level - 0 stands for no debug messages, verbosity increases with the level |
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.
A vector of values of slicing index for each probeset - the further from 0, the more significant splicing. Or a table with names of genes, exon, probesets, expression and splicing index.
Michal J Okoniewski
http://bioinformatics.picr.man.ac.uk/
## Not run: gg <- probeset.to.gene(c("2326780","2326822" )) spl.idx <- splicing.index(x.rma, gg, "group", c("a","b"), debug=4) ## End(Not run)