wilcox_score-methods: Methods for Function 'wilcox_score' in Package 'gCMAP'

In gCMAP: Tools for Connectivity Map-like analyses

Description

These methods provide a wrapper for the Mean-rank Gene Set Test function wilcoxGST

wilcox_score is a synonym for gst_score with ranks.only=TRUE. This test procedure was developed by Michaud et al (2008), who called it mean-rank gene-set enrichment.

Usage

## S4 method for signature 'matrix,CMAPCollection'
wilcox_score(experiment, sets, adjust.ties=FALSE, keep.scores=FALSE, ...)

## S4 method for signature 'numeric,CMAPCollection'
wilcox_score(experiment, sets,...)

## S4 method for signature 'eSet,CMAPCollection'
wilcox_score(experiment, sets, element="z",...)

## S4 method for signature 'matrix,GeneSet'
wilcox_score(experiment, sets,...)

## S4 method for signature 'numeric,GeneSet'
wilcox_score(experiment, sets,...)

## S4 method for signature 'eSet,GeneSet'
wilcox_score(experiment, sets, element="z",...)

## S4 method for signature 'matrix,GeneSetCollection'
wilcox_score(experiment, sets,...)

## S4 method for signature 'numeric,GeneSetCollection'
wilcox_score(experiment, sets,...)

## S4 method for signature 'eSet,GeneSetCollection'
wilcox_score(experiment, sets, element="z",...)

## S4 method for signature 'CMAPCollection,eSet'
wilcox_score(experiment, sets, element="z",adjust.ties=FALSE, keep.scores=FALSE,...)

## S4 method for signature 'CMAPCollection,numeric'
wilcox_score(experiment, sets,...)

## S4 method for signature 'CMAPCollection,matrix'
wilcox_score(experiment, sets,...)

## S4 method for signature 'GeneSet,numeric'
wilcox_score(experiment, sets,...)

## S4 method for signature 'GeneSet,matrix'
wilcox_score(experiment, sets,...)

## S4 method for signature 'GeneSet,eSet'
wilcox_score(experiment, sets,element="z",...)

## S4 method for signature 'GeneSetCollection,numeric'
wilcox_score(experiment, sets,...)

## S4 method for signature 'GeneSetCollection,matrix'
wilcox_score(experiment, sets,...)

## S4 method for signature 'GeneSetCollection,eSet'
wilcox_score(experiment, sets,element="z",...)

Arguments

sets	A CMAPCollection, GeneSetCollection or GeneSet object containing gene sets, with which to query the experiment object.
experiment	An eSet or matrix or vector with numeric data to compare the query object to.
element	Character vector specifying which channel of an eSet to extract (defaults to "exprs", alternatives may be e.g. "z", etc.)
...	Additional arguments passed on to downstream methods.
adjust.ties	Logical: adjust Wilcox-Mann-Whitney statistic in the presence of ties ? (Default: FALSE)
keep.scores	Logical: keep gene-level scores for all gene sets (Default: FALSE) ? The size of the generated CMAPResults object increases with the number of contained gene sets. For very large collections, setting this parameter to 'TRUE' may require large amounts of memory.

Value

A CMAPResult object

Examples

data(gCMAPData)
gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)

profile <- assayDataElement(gCMAPData[,1], "z")
## one profile versus three sets
wilcox_score(profile, gene.set.collection)

## three sets versus three profiles
wilcox_score(gene.set.collection, gCMAPData)

gCMAP documentation built on April 29, 2020, 3:54 a.m.