plotP {SPIA}R Documentation

SPIA two-way evidence plot

Description

Plots each pathway as a point, using the over-representation p-value, pNDE, and perturbations accumulation p-value, pPERT, as coordinates.

Usage

plotP(x,threshold=0.05)

Arguments

x A data frame produced by spia function.
threshold A numerical value between 0 and 1 to be used as significance threshold in inferring pathway significance.

Details

In this plot each pathway is a point and the coordinates are the log of pNDE (using a hypergeometric model) and the p-value from perturbations, pPERT. The oblique lines in the plot show the significance regions based on the combined evidence.

Value

This function does not return any value. It only generates a plot.

Author(s)

Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Khatri, Sorin Draghici

References

Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82.

See Also

spia

Examples

# Examples use colorectal cancer dataset
data(colorectalcancer)

# pathway analysis based on combined evidence of ORA and perturbations
# use nB=2000 or larger for more accurate results
res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",nB=200,plots=FALSE,verbose=TRUE,beta=NULL)

#Generate the evidence plot
plotP(res,threshold=0.1)

[Package SPIA version 1.0.0 Index]