si {exonmap}R Documentation

Calculate the splicing index

Description

Calculates the splicing index for the probesets in one or more genes, as defined in the Affymetrix white paper "Alternative Transcript Analysis Methods for Exon Arrays".

Usage

 si(x, v, group, gps, median.gene=FALSE,median.probeset=FALSE,unlogged=TRUE)

Arguments

x eSet containing expression data
v Character vector of Ensembl gene names
group If defined, the column name in the ExpressionSet's pData object in which to look for gps
gps The two sets of arrays to compare
median.gene Use the median instead of the mean when calculating averages across genes
median.probeset Use the median instead of the mean when calculating averages across probesets in each replicate group
unlogged Unlog the expression data before calculating the splicing index (and then re-log afterwards)

Details

The splicing index gives a measure of the difference in expression level for each probeset in a gene between two sets of arrays, relative to the gene-level average in each set. This is calculated only for those probesets that are defined as exon targeting and non-multitargetted (See select.probewise and exclude.probewise for more details of how this filtering is performed.

The two sets of arrays can be specified in two ways: First, by using numeric indices defining the appropriate columns in the expression data. This is done by supplying these as a list to gps (e.g. gps=list(1:3,4:6) will calculate the splicing index between arrays 1,2,3 and 4,5,6. Alternatively, the annotation in the pData object from x can be used (e.g. group="treatment",gps=c("a","b"), will compare between the arrays labelled "a", and "b" in the "treatment" column of pData(x)).

The implementation also calculates a p.value and t.statistic for each probeset; these are returned alongside the splicing index.

By default, the splicing index is calculated using the mean across genes and samples. Specifing median.gene=TRUE or median.probeset=TRUE will use the median instead (for the gene or probeset level averages, respectively). It is calculated using the unlogged data, unless unlogged=FALSE. This only affects the internal calculations; values in x are always assumed to be logged, and the splicing index is always returned on the log2 scale.

Value

A list, one element for each gene. Each element contains a data.frame, with the results for a given gene. Each row corresponds to a probeset, and there are four columns in the data.frame: "si","p.value","t.statistic" and "gene.av".

Author(s)

Crispin J Miller with contributions from Carla Moller Levet and Michal J Okoniewski

References

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

See Also

splanova

Examples

 
  if(interactive()) {
    xmapConnect()
    data(exonmap)
    gg <- probeset.to.gene(c("2326780","2326822" ))
    spl.idx <-  si(x, gg, "group", c("a","b"))
    spl.idx <-  si(x, gg, gps=list(1:3,4:6))
  }

[Package exonmap version 2.0.03 Index]