absoluteTest.genePvals: A function to calculate the P values for each gene as...
In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

Description Usage Arguments Value

A function to calculate the P values for each gene as compared with either 0, the gene set mean, or the full PDF of the gene set.

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absoluteTest.genePvals(QSarray, path.index = 1:numPathways(QSarray),
  silent = TRUE, FastApproximated = TRUE, addVIF = !is.null(QSarray$vif),
  NPoints = QSarray$n.points/8, compareTo = c("zero", "mean", "pdf"))

`QSarray`	A QSarray object, as generated by aggregateGeneSet and possibly modified by calcVIF
`path.index`	The pathways to calculate the pVals for.
`silent`	If false, print a "." every fifth pathway, as a way to keep track of progress
`FastApproximated`	fast mode which uses normal approximations for the PDF's
`addVIF`	Whether to include the VIF in the calculation of the p-values. By default, if the VIF has been calculated, it will be used
`NPoints`	points to use
`compareTo`	the null hypothesis that each gene set is tested against.