pumaPCARes-class: Class pumaPCARes

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

This is a class representation for storing the outputs of the pumaPCA function. Objects of this class should usually only be created through the pumaPCA function.

Objects from the Class

Objects can be created by calls of the form new("pumaPCARes", ...).

Slots

model:

Object of class "pumaPCAModel" representing the model parameters

expectations:

Object of class "pumaPCAExpectations" representing the model expectations

varY:

Object of class "matrix" representing the variance in the expression levels

Y:

Object of class "matrix" representing the expression levels

phenoData:

Object of class "AnnotatedDataFrame" representing the phenotype information

timeToCompute:

Object of class "numeric" representing the time it took pumaPCA to run

numberOfIterations:

Object of class "numeric" representing the number of iterations it took pumaPCA to converge

likelihoodHistory:

Object of class "list" representing the history of likelihood values while pumaPCA was running

timingHistory:

Object of class "list" representing the history of how long each iteration took while pumaPCA was running

modelHistory:

Object of class "list" representing the history of how the model was changing while pumaPCA was running

exitReason:

Object of class "character" representing the reason pumaPCA halted. Can take the values "Update of Likelihood less than tolerance x", "Update of W less than tolerance x", "Iterations exceeded", "User interrupt", "unknown exit reason"

Methods

plot

signature(x="pumaPCARes-class"): plots two principal components on a scatter plot.

write.reslts

signature(x = "pumaPCARes-class"): writes the principal components for each array to a file. It takes the same arguments as write.table. The argument "file" does not need to set any extension. The file name and extension "csv" will be added automatically. The default file name is "tmp".

Author(s)

Richard D. Pearson

See Also

Related method pumaPCA and related class pumaPCARes.

puma documentation built on Nov. 8, 2020, 11:08 p.m.