Last data update: 2014.03.03
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R: Plot Pathway-Express result
plot,peRes,missing-method | R Documentation |
Plot Pathway-Express result
Description
Display a two-way plot using two of the p-values from the Pathway-Express analysis.
Usage
## S4 method for signature 'peRes,missing'
plot(x, y, ..., comb.pv.func = compute.fisher,
adjust.method = "fdr", threshold = 0.05, eps = 1e-06)
## S4 method for signature 'peRes,character'
plot(x, y, ..., comb.pv.func = compute.fisher,
adjust.method = "fdr", threshold = 0.05, eps = 1e-06)
Arguments
x |
an object of type peRes-class
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y |
vector of two p-values names to be combined using comb.pv.func (default: c("pAcc", "pORA") ).
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... |
Arguments to be passed to methods, such as par .
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comb.pv.func |
the function to combine the p-values - takes as input a vector of p-values
and returns the combined p-value (default: compute.fisher ).
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adjust.method |
the name of the method to adjust the p-value (see p.adjust )
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threshold |
corrected p-value threshold
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eps |
any value smaller than this will be considered as eps (default: 1e-6 ).
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Author(s)
Calin Voichita and Sorin Draghici
See Also
pe , summary.peRes , plot,pePathway,missing-method
Examples
# load experiment
load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))
fc <- top$logFC[top$adj.P.Val <= .01]
names(fc) <- top$entrez[top$adj.P.Val <= .01]
ref <- top$entrez
# load the set of pathways
kpg <- keggPathwayGraphs("hsa")
kpg <- setEdgeWeights(kpg)
kpg <- setNodeWeights(kpg, defaultWeight = 1)
# perform the pathway analysis (for more accurate results use nboot = 2000)
peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)
plot(peRes)
plot(peRes, c("pPert","pORA"), comb.pv.func = compute.normalInv, threshold = .01)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ROntoTools)
Loading required package: graph
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: boot
Loading required package: KEGGREST
Loading required package: KEGGgraph
Attaching package: 'KEGGgraph'
The following object is masked from 'package:graphics':
plot
Loading required package: Rgraphviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ROntoTools/plot.peRes-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot,peRes,missing-method
> ### Title: Plot Pathway-Express result
> ### Aliases: plot,peRes,character-method plot,peRes,missing-method
>
> ### ** Examples
>
>
> # load experiment
> load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))
> fc <- top$logFC[top$adj.P.Val <= .01]
> names(fc) <- top$entrez[top$adj.P.Val <= .01]
> ref <- top$entrez
>
> # load the set of pathways
> kpg <- keggPathwayGraphs("hsa")
Using cached pathway data. Database info:
pathway KEGG Pathway Database
path Release 73.0+/01-03, Jan 15
Kanehisa Laboratories
343,170 entries
Default parameters detected. Using pre-parsed data.
> kpg <- setEdgeWeights(kpg)
> kpg <- setNodeWeights(kpg, defaultWeight = 1)
>
> # perform the pathway analysis (for more accurate results use nboot = 2000)
> peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)
Performing pathway analysis...
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>
> plot(peRes)
>
> plot(peRes, c("pPert","pORA"), comb.pv.func = compute.normalInv, threshold = .01)
Warning message:
In max(st[i, "pComb"]) : no non-missing arguments to max; returning -Inf
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> dev.off()
null device
1
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