R Graphical Manual

Last data update: 2014.03.03

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SPIA-internal (Package: SPIA) : Internal SPIA functions

Internal SPIA functions. getP2 given a pG returns two equal p-values such as combfunc(p1,p2)=pG.

● Data Source: BioConductor
● Keywords: internal
● Alias: getP2
● 0 images

combfunc (Package: SPIA) : Combining two p-values using Fisher's product or normal inversion method

Combining two p-values using Fisher's product or normal inversion methods.

● Data Source: BioConductor
● Keywords: methods, nonparametric
● Alias: combfunc
● 0 images

makeSPIAdata (Package: SPIA) : Process KGML files for spia analysis

This function processes KEGG xml files into a xxxSPIA.RData file needed for spia function.

● Data Source: BioConductor
● Keywords: methods, nonparametric
● Alias: makeSPIAdata
● 0 images

plotP (Package: SPIA) : 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.

● Data Source: BioConductor
● Keywords: methods, nonparametric
● Alias: plotP
● 2 images

spia (Package: SPIA) : Signaling Pathway Impact Analysis (SPIA) based on over-representation and signaling perturbations accumulation

This function implements the SPIA algorithm to analyze KEGG signaling pathways.

● Data Source: BioConductor
● Keywords: methods, nonparametric
● Alias: spia
● 2 images