SPIA two-way evidence plot
Plots each pathway as a point, using the over-representation p-value, pNDE, and perturbations accumulation p-value, pPERT, as coordinates. In addition the regions where FDR and FWER adjusted pG values are less than the specified threshold are plotted. The function determines automatically which method (fisher or norminv) was used to combine the two p-values into pG, and plots the regions described above accordingly.
- A data frame produced by
- 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 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,combine="fisher") #Generate the evidence plot plotP(res,threshold=0.1) res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",nB=200,plots=FALSE,verbose=TRUE,beta=NULL,combine="norminv") #Generate the evidence plot plotP(res,threshold=0.1)