qusageArm: This file contains the primary code for the qusage...

In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression

Description

This file contains the primary code for the qusage methodology Author: Christopher Bolen Gur Yaari (c) 2013 Yale University. All rights reserved. but runs welch's approximation in C++.

Usage

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

Arguments

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

Value

qusage data array for welch's approx

arcolombo/junk documentation built on May 10, 2019, 12:49 p.m.