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, median.gene=TRUE, vector.out=TRUE, by.chip=FALSE)
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 |
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 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.
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")) ## End(Not run)