runSPIA: Run SPIA analysis
In sales-lab/graphite: GRAPH Interaction from pathway Topological Environment

runSPIA

R Documentation

Run SPIA analysis

Description

Run a topological analysis on an expression dataset using SPIA.

Usage

  runSPIA(de, all, pathwaySetName, ...)

Arguments

`de`	A named vector containing log2 fold-changes of the differentially expressed genes. The names of this numeric vector are Entrez gene IDs.
`all`	A vector with the Entrez IDs in the reference set. If the data was obtained from a microarray experiment, this set will contain all genes present on the specific array used for the experiment. This vector should contain all names of the 'de' argument.
`pathwaySetName`	The name of a pathway set created with `prepareSPIA`.
`...`	Additional options to pass to `spia`.

Details

The spia option "organism" is internally used. It is an error use it in the additional options.

Value

The same of spia, without KEGG links. A data frame containing the ranked pathways and various statistics: pSize is the number of genes on the pathway; NDE is the number of DE genes per pathway; tA is the observed total preturbation accumulation in the pathway; pNDE is the probability to observe at least NDE genes on the pathway using a hypergeometric model; pPERT is the probability to observe a total accumulation more extreme than tA only by chance; pG is the p-value obtained by combining pNDE and pPERT; pGFdr and pGFWER are the False Discovery Rate and respectively Bonferroni adjusted global p-values; and the Status gives the direction in which the pathway is perturbed (activated or inhibited).

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.

Examples

if (require(SPIA) && require(hgu133plus2.db)) {
  data(colorectalcancer)

  top$ENTREZ <- mapIds(hgu133plus2.db, top$ID, "ENTREZID", "PROBEID", multiVals = "first")
  top <- top[!is.na(top$ENTREZ) & !duplicated(top$ENTREZ), ]
  top$ENTREZ <- paste("ENTREZID", top$ENTREZ, sep = ":")
  tg1 <- top[top$adj.P.Val < 0.05, ]

  DE_Colorectal = tg1$logFC
  names(DE_Colorectal) <- tg1$ENTREZ
  ALL_Colorectal <- top$ENTREZ

  kegg <- pathways("hsapiens", "kegg")[1:20]
  kegg <- convertIdentifiers(kegg, "ENTREZID")
  prepareSPIA(kegg, "keggEx")
  runSPIA(de = DE_Colorectal, all = ALL_Colorectal, "keggEx")

  unlink("keggExSPIA.RData")
}

sales-lab/graphite documentation built on Oct. 15, 2023, 9:23 a.m.