This function takes a ranked gene expression matrix obtained from rankGenes() function and a GeneSet object as input parameters. It returns a data.frame consists of calculated scores and dispersions for each sample. It is suggested to use the generic version of of this method which can work with gene set stored in both vector or GeneSet.

singscoring(rankData, upSet, downSet = NULL, subSamples = NULL,
  centerScore = TRUE, dispersionFun = mad)

Arguments

rankData

A matrix, ranked gene expression matrix data

upSet

A GeneSet object, up regulated gene set

downSet

A GeneSet object, down regulated gene set

subSamples

A character or vector of sample labels/indices that will be used to subset the rankData matrix.All samples will be scored by default.

centerScore

A Boolean, specifying whether scores should be centred

dispersionFun

A function, dispersion function with default as 'mad'

Value

A data.frame consists of scores and dispersions for all samples

See also

simpleScore() "GeneSet"