Class "QSarray"

Description

A list-based 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. x-coordinates 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 x-coordinates of the PDF are the sequence of n.points from path.mean-ranges 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 or makeComparison. See newQSarray 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 (if numPathways < 10) or plotCIs (if numPathways >= 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