Class "QSarray"
Description
A listbased class which contains the results of running qusage. Generally created by qusage
or makeComparison
Objects from the Class
QSarray objects should not be created directly, but rather through the makeComparison
function. They can also be created manually via a call to the newQSarray
function, although this should be done by advanced users only.
Components
QSarray
objects do not contain any slots (apart from .Data
) but they should contain the following list components:
mean  numeric vector containing mean fold changes for individual genes 
SD  numeric vector of standard deviations for individual genes 
dof  numeric vector. Degrees of Freedom for each gene 
var.method  one of ("Welch's","Pooled") , indicating the method used to calculate the variance 
sd.alpha  The factor each sd is multiplied by (either due to the min.variance.factor parameter in makeComparison or because of the Bayesian shrinkage of the SDs). This is used when calculating the VIF in order to correct for genes with 0 (or very small) variance. 
labels  The labels as input in makeComparisons, describing the group structure of the data. 
pairVector  A vector indicating which samples should be treated as pairs. 
contrast  A string describing which of the two groups in labels was compared. 
The following additional components are appended to the object by running aggregateGeneSet
and calcVIF
pathways  the list of genes in each gene set. Represented as a list of indices. 
path.mean  vector describing the mean fold change for each of the pathways provided to AggregateGeneSet 
path.PDF  Matrix describing the probability distributions for each of the pathways provided to AggregateGeneSet, where each column is a different gene set, and each row is a different point where this set was sampled. xcoordinates must be generated using getXcoords 
path.size  numeric vector containing the number of features in each pathway that mapped to the input data. 
ranges  the (uncorrected) range that all PDFs were calculated over. If the VIF is not used to correct the range, the xcoordinates of the PDF are the sequence of n.points from path.meanranges to path.mean+ranges 
n.points  The number of points that the PDF was calculated at. This is equal to the number of rows in path.PDF 
vif  the Variance Inflation Factor for each pathway, as calculated by calcVIF

Methods
 newQSarray
The constructor for the QSarray object. Should primarily be used internally by
qusage
ormakeComparison
. SeenewQSarray
for additional details. numFeatures
Returns the number of features (i.e. genes or probesets) in the dataset
 numPathways
Returns the number of pathways provided to
aggregateGeneSet
 dim
dimensions of the QSarray object, as c(numFeatures, numPathways)
 print, head
Prints a summarized version of all fields in the QSarray object.
 summary
Prints a brief summary of the QSarray object.
 plot
Plots the information stored in QSarray by either calling
plotDensityCurves
(ifnumPathways
< 10) orplotCIs
(ifnumPathways
>= 10) qsTable
Print a table with a summary of the information on the most significant gene sets in QSarray. See
qsTable
for more details.
Author(s)
Christopher Bolen