annmap.spliceIndex: Splice indexing

In annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

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

  spliceGroupIndex( x, group.column, members )
  spliceIndex( x, ids, group, gps, group.index.fn=spliceGroupIndex, median.gene=FALSE, median.probeset=FALSE, unlogged=TRUE )

Arguments

x	eSet containing expression data
group.column	a column name for the group data
members	a set of arrays
ids	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
group.index.fn	a method which, when passed an ExpressionSet (from the Biobase package), a column name for the group data and a set of arrays, will return the indices of interest
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 exonic (See exonic).

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 phenoData 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. Specifying 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.

Author(s)

Tim Yates Crispin J. Miller

See Also

exonic

Examples

  if(interactive()) {
    # Loads the Expression Set into x.rma
    load( '../unitTests/HuEx-1_0.tp53.expr.RData' )
    spliceIndex( x.rma, symbolToGene( 'tp53' ), gps=list(1:3,4:6) )
  }

annmap documentation built on Nov. 8, 2020, 7:43 p.m.