Function to use SPIA method on microarray or RNA-Seq data

Description

The function runs SPIA method on microarray or RNA-Seq data. The implementatio includes the identification of differentially expressed genes and transformation of pathways' topologies to an appropriate form. The SPIA method combines two independent p-values. One p-value comes from overrepresentation analysis and the other is so called pertubation factor.

Usage

SPIA(x, group, pathways, type, preparePaths=TRUE, norm.method=NULL, test.method=NULL, p.th=0.05, logFC.th=2, nperm=1000, combine="fisher", 
 both.directions=TRUE, maxNodes=150, minEdges=0, commonTh=2, filterSPIA=FALSE, convertTo="none", convertBy=NULL)

Arguments

Value

A list:

Author(s)

Ivana Ihnatova

References

Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009 Jan 1;25(1):75-82.

Adi L. Tarca, Sorin Draghici, Purvesh Khatri, et. al, A Signaling Pathway Impact Analysis for Microarray Experiments, 2008, Bioinformatics, 2009, 25(1):75-82.

Draghici, S., Khatri, P., Tarca, A.L., Amin, K., Done, A., Voichita, C., Georgescu, C., Romero, R.: A systems biology approach for pathway level analysis. Genome Research, 17, 2007.

See Also

preparePathways

Examples

if (require(DEGraph)) {
  data("Loi2008_DEGraphVignette")
 pathways<-pathways("hsapiens","biocarta")[1:10]
  SPIA(exprLoi2008, classLoi2008,pathways, type="MA", logFC.th=-1)
}
## Not run: 
if (require(gageData)) {

 data(hnrnp.cnts)
  hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
 group<-c(rep("sample",4), rep("control",4))
 
  pathways<-pathways("hsapiens","biocarta")[1:10]
 SPIA( hnrnp.cnts, group, pathways, type="RNASeq",  logFC.th=-1, IDs="entrez", test="vstlimma")
 }

## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ToPASeq)
Loading required package: graphite
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: gRbase
Loading required package: graph
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: Rgraphviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ToPASeq/SPIA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SPIA
> ### Title: Function to use SPIA method on microarray or RNA-Seq data
> ### Aliases: SPIA
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> if (require(DEGraph)) {
+   data("Loi2008_DEGraphVignette")
+  pathways<-pathways("hsapiens","biocarta")[1:10]
+   SPIA(exprLoi2008, classLoi2008,pathways, type="MA", logFC.th=-1)
+ }
Loading required package: DEGraph
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'DEGraph'
> ## Not run: 
> ##D if (require(gageData)) {
> ##D 
> ##D  data(hnrnp.cnts)
> ##D   hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
> ##D  group<-c(rep("sample",4), rep("control",4))
> ##D  
> ##D   pathways<-pathways("hsapiens","biocarta")[1:10]
> ##D  SPIA( hnrnp.cnts, group, pathways, type="RNASeq",  logFC.th=-1, IDs="entrez", test="vstlimma")
> ##D  }
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>