plotP {SPIA} | R Documentation |
Plots each pathway as a point, using the over-representation p-value, pNDE, and perturbations accumulation p-value, pPERT, as coordinates.
plotP(x,threshold=0.05)
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. |
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.
This function does not return any value. It only generates a plot.
Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Khatri, Sorin Draghici
Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for
Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82.
# 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)