mwwGST: Competitive Gene Set Test

In miccec/yaGST: Competitive gene set and regulon tests.

Description

Run a competitive test to highlight whether a gene set is highly ranked in a sequence of gene values on the genes outside the gene-set.

Usage

mwwGST(rankedList, geneSet, minLenGeneSet = 5, alternative = "greater", moreDetails = FALSE, verbose = TRUE)

Arguments

rankedList	numeric vector of data values where the names are the genes names
geneSet	a character list of genes
minLenGeneSet	minimum dimension of the geneSet
alternative	a character string specifying the alternative hypothesis ("two.sided", "less", "greater").
moreDetails	a logical indicating whether the output includes the rankedList (necessary to plot the enrichment)
verbose	a logical indicating to suppress or not the messages; it's TRUE by default.

Value

call	a character string of the call of the function.
alternative	a character string describing the alternative hypothesis.
originalGeneSetCount	the length of the gene-set given in input
actualGeneSet	the list of genes as comes from the intesection between the gene-set and the ranked-list.
actualGeneSetCount	the length of the actualGeneSet
rankedList	the ranked-list given in input; this slot is filled whether moreDetails is TRUE
lengthOfRankedList	the length of the ranked-list given in input
statistic	the value of the Mann-Whitney-Wilcox test statistic.
nes	the value of the normalized enrichment score.
pu	is the probability unbalance, i.e. the ratio of nes to 1-nes.
log.pu	the log2 transformation of the pu.
p.value	the p-value for the test.

Author(s)

Stefano M. Pagnotta

See Also

rankedList, mwwExtGST

Examples

  library(yaGST)
  data("rankedList")
  # generate a random data set of dimension 100
  geneSet <- sample(head(names(rankedList), 5000), 100)
  ans <- mwwGST(rankedList, geneSet, moreDetails = TRUE)
  ans
  plot(ans)
  
  # generate a second gene set
  geneSet <- sample(tail(names(rankedList), 5000), 100)
  ans <- mwwGST(rankedList, geneSet, moreDetails = TRUE)
  plot(ans)

miccec/yaGST documentation built on May 23, 2019, 7:35 a.m.