makeSPIAdata: Process KGML files for spia analysis

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

Description

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

Usage

makeSPIAdata(kgml.path="./hsa",organism="hsa",out.path=".")

Arguments

kgml.path	Character vector giving the location of the folder containing two or more KEGG xml files. See for e.g. http://www.genome.jp/kegg/pathway/hsa/hsa04010.html and click the Download KGML to get such files. Users that have a license to the KEGG ftp directory can copy all the xml files corresponding to a givne organism.
organism	A three letter character designating the organism. See a full list at ftp://ftp.genome.jp/pub/kegg/xml/organisms.
out.path	Directory where a "organism"SPIA.RData file will be saved. If left to null, it will will try to save the file in th extdata folder of the SPIA library.

Author(s)

Adi Laurentiu Tarca <[e-mail]>

See Also

spia

Examples

library(SPIA)
data(colorectalcancer)
makeSPIAdata(kgml.path=system.file("extdata/keggxml/hsa",package="SPIA"),organism="hsa",out.path="./")
res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",data.dir="./")
res[,-12]

SPIA documentation built on Nov. 8, 2020, 5:44 p.m.