runPathwayAnalysis | R Documentation |
This function performs patwhay analysis using SPIA, CePaORA, and CePaGSA methods.
runPathwayAnalysis(
summarizedExperiment,
network,
method = c("spia", "cepaORA", "cepaGSA"),
SPIAArgs = list(all = NULL, nB = 2000, verbose = TRUE, beta = NULL, combine = "fisher",
pThreshold = 0.05),
CePaORAArgs = list(bk = NULL, cen = c("equal.weight", "in.degree", "out.degree",
"betweenness", "in.reach", "out.reach"), cen.name = c("equal.weight", "in.degree",
"out.degree", "betweenness", "in.reach", "out.reach"), iter = 1000, pThreshold =
0.05),
CePaGSAArgs = list(cen = c("equal.weight", "in.degree", "out.degree", "betweenness",
"in.reach", "out.reach"), cen.name = c("equal.weight", "in.degree", "out.degree",
"betweenness", "in.reach", "out.reach"), nlevel = "tvalue_abs", plevel = "mean", iter
= 1000)
)
summarizedExperiment |
The generated SummarizedExpriment object from DE analysis result. |
network |
The pathways network object. |
method |
The pathway analsyis method, including SPIA, cepaORA, and cepaGSA. |
SPIAArgs |
A list of other passed arguments to spia. See spia function. |
CePaORAArgs |
A list of other passed arguments to CePaORA. See CePa function. |
CePaGSAArgs |
A list of other passed arguments to CePaGSA. See CePa function. |
A dataframe of pathway analysis result, which contains the following columns
ID: The ID of the gene set
p.value: The p-value of the gene set
pFDR: The adjusted p-value of the gene set using the Benjamini-Hochberg method
score: The enrichment score of the gene set
normalizedScore: The normalized enrichment score of the gene set
sampleSize: The total number of samples in the study
name: The name of the gene set
pathwaySize: The size of the gene set
library(RCPA)
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")
spiaNetwork <- loadData("spiaNetwork")
cepaNetwork <- loadData("cepaNetwork")
spiaResult <- runPathwayAnalysis(RNASeqDEExperiment, spiaNetwork, method = "spia")
cepaORAResult <- runPathwayAnalysis(RNASeqDEExperiment, cepaNetwork, method = "cepaORA")
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