Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

---

Documentation for package ‘SPIA’ version 2.54.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ALL_Colorectal	Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
ALL_Vessels	Results from a microarray expriment comparing umbilical veins and arteries tissues
colorectalcancer	Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
combfunc	Combining two p-values using Fisher's product or normal inversion method
DE_Colorectal	Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
DE_Vessels	Results from a microarray expriment comparing umbilical veins and arteries tissues
makeSPIAdata	Process KGML files for spia analysis
plotP	SPIA two-way evidence plot
spia	Signaling Pathway Impact Analysis (SPIA) based on over-representation and signaling perturbations accumulation
top	Results from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
Vessels	Results from a microarray expriment comparing umbilical veins and arteries tissues