simpleScore {singscore} | R Documentation |
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 signature 'ANY,vector,missing' simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) ## S4 method for signature 'ANY,GeneSet,missing' simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) ## S4 method for signature 'ANY,vector,vector' simpleScore(rankData, upSet, downSet = NULL, subSamples = NULL, centerScore = TRUE, dispersionFun = mad, knownDirection = TRUE) ## S4 method for signature 'ANY,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 |
dispersionFun |
A function, dispersion function with default being |
knownDirection |
A boolean flag, it deterimines whether the scoring method should derive the scores in a directional mannar when the gene signature only contains one set of gene set (passing the gene set via upSet). It is default as TRUE but one can set the argument to be FALSE to derive the score for a single gene set in a undirectional way. This parameter becomes irrelevant when both upSet and downSet are provided. |
A data.frame consists of singscores and dispersions for all samples
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.