Description Usage Arguments Value Examples
Main Function for pathway analysis
The PathAnalysis
is a function to perform pathway analysis
(a.k.a. gene set enrichment test) for functional annotation of a candidate
gene list or an ordered gene result from Meta DE analysis output.
1 2 3 4 | PathAnalysis(meta.p = NULL, pathway = c(Biocarta.genesets, GOBP.genesets,
GOCC.genesets, GOMF.genesets, KEGG.genesets, Reactome.genesets),
enrichment = c("KS", "Fisher's exact"), p.cut = NULL,
DEgene.number = 200, size.min = 15, size.max = 500)
|
meta.p |
is a vector of meta-analysis p-value. |
pathway |
is a vector of pathway databases used for functional analysis, see data(pathways) for more details. |
enrichment |
is the method used for pathway analysis, must be one of "KS" and "Fisher's exact". |
p.cut |
is the p-value cutoff to select the DE genes, option for Fisher's exact method only. |
DEgene.number |
is the top number of DE genes, option for Fisher's exact method only. |
size.min |
is the minimum pathway size to be included in the functional analysis. |
size.max |
is the maximum pathway size to be included in the functional analysis. |
a data frame with columns:
pvalue the p-value from pathway analysis for each pathway
qvalue the q-value from pathway analysis for each pathway
OddsRatio optional, the odds ratio from Fisher's exact test method
logOR optional, the log odds ratio from Fisher's exact test method
DEgenes optional, the set of DE genes in each pathway
1 2 3 4 5 6 | ## Not run:
meta.p <- meta.res$meta.analysis$pval
ks.result <- PathAnalysis(meta.p = meta.p, enrichment = "KS")
fisher.result <- PathAnalysis(meta.p = meta.p, enrichment = "Fisher's exact")
## End(Not run)
|
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