qusageCutArm: This file contains the primary code for the qusage...
In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

1 2	qusageCutArm(eset, labels, contrast, geneSets, pairVector = NULL, var.equal = FALSE, filter.genes = FALSE, n.points = 2^12)

`eset`	a matrix of log2(expression values), with rows of features and columns of samples. OR an object of class ExpressionSet
`labels`	vector of labels representing each column of eset.
`contrast`	a string describing which of the groups in 'labels' we want to compare. This is usually of the form 'trt-ctrl', where 'trt' and 'ctrl' are groups represented in 'labels'.
`geneSets`	a list of pathways to be compared. Each item in the list is a vector of names that correspond to the row names of eset.
`pairVector`	A vector of factors (usually just 1,2,3,etc.) describing the sample pairings. This is often just a vector of patient IDs or something similar. If not provided, all samples are assumed to be independent.
`var.equal`	a logical variable indicating whether to treat the two variances as being equal. If TRUE then the pooled variance is used to estimate the variance otherwise the Welch approximation is used.
`filter.genes`	a boolean indicating whether the genes in eset should be filtered to remove genes with low mean and sd.
`n.points`	The number of points to sample the convolution at. Passed to aggregateGeneSet