simpleScore.Rd
This function computes 'singscores' using a ranked gene
expression matrix obtained from the rankGenes()
function and a gene set or
a pair of up-regulated and down-regulated gene sets. It returns a data.frame
of scores and dispersions for each sample. The gene sets can be in vector
format or as GeneSet objects (from GSEABase packages). If samples need to be
scored against a single gene set, the upSet
argument should be used
to pass the gene set while the downSet
argument is set to
NULL
. This setting is ideal for gene sets representing gene
ontologies where the nature of the genes is unknown (up- or down-regulated).
simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) # S4 method for matrix,vector,missing simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) # S4 method for matrix,GeneSet,missing simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) # S4 method for matrix,vector,vector simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) # S4 method for matrix,GeneSet,GeneSet simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE)
rankData | A matrix object, ranked gene expression matrix data generated
using the |
---|---|
upSet | A GeneSet object or character vector of gene IDs of up-regulated gene set or a gene set where the nature of genes is not known |
downSet | A GeneSet object or character vector of gene IDs of down-regulated gene set or NULL where only a single gene set is provided |
subSamples | A vector of sample labels/indices that will be used to subset the rankData matrix. All samples will be scored if not provided |
centerScore | A Boolean, specifying whether scores should be centered
around 0, default as TRUE. Note: scores never centered if |
dispersionFun | A function, dispersion function with default being |
knownDirection | A boolean, determining whether the gene set should be considered to be directional or not. A gene set is directional if the type of genes in it are known i.e. up- or down-regulated. This should be set to TRUE if the gene set is composed of both up- AND down-regulated genes. Defaults to TRUE. This parameter becomes irrelevant when both upSet(Colc) and downSet(Colc) are provided. |
A data.frame consists of singscores and dispersions for all samples
rank
"GeneSet"
ranked <- rankGenes(toy_expr_se) scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn) # toy_gs_up is a GeneSet object, alternatively a vector of gene ids may also # be supplied.