geNetClassifier (version 1.12.0)

plot.GenesRanking: Plot GenesRanking

Description

Plots the posterior probability of the genes ordered by class ranking.

Usage

"plot"(x, y="missing", numGenesPlot=1000,  plotTitle="Significant genes", lpThreshold = 0.95, ...)

Arguments

x

GenesRanking.

numGenesPlot

Numeric. Number of genes to plot.

plotTitle

Character. Plot main title.

lpThreshold

Numeric between 0 and 1. Required posterior probability value to consider a gene 'significant'.

y

Not required.

...

Not required

Value

Posterior probability plot of the top genes.

Details

Significant genes: Genes with posterior probability over 'lpThreshold'. More significant genes may mean:

• Very different class
• More systemic disease

Plot lines represet the posterior probability of genes, sorted by rank from left to right.

In order to find genes that diferentiate the classes from each other, the function ranks the genes bassed on their posterior probability for each class. The posterior probability represents how well a gene differentiates samples from a class, from samples from other classes. Therefore, Genes with high posterior probability are good to differentiate a class from all the others. This posterior probability is calculated by emfit (pkg:EBarrays), an expectation-maximization (EM) algorithm for gene expression mixture model.

Examples

# Load or calculate a ranking (or a classifier with geNetClassifier)
data(leukemiasClassifier) # Sample trained classifier, @genesRanking

# Default plot:
plot(leukemiasClassifier@genesRanking)

# Changing options:
plot(leukemiasClassifier@genesRanking, 
    numGenesPlot=5000, plotTitle="Leukemias", lpThreshold=0.9)