Performs the non-parametric rank product test on the intensity data.
Usage
RankProduct(dataset, listofargs)
Arguments
dataset
an R data frame generated with generateDatasetFile
listofargs
a list containing:
- the number of permutations to perform to compute the p-values (usually 100)
- 1 or 2, depending if the search is for a significant decrease or increase
- a character string specifying the column whose values will be used for the test
- a character string specifying the name of the dataset column to be used to define the replicate, for example "GeneName" or "Internal_GeneID"
Value
Returns a list containing
pValVec
a named vector of p-values
dataset
the dataset with an added column "p.value.rankproduct"
paste("pValue.rankproduct", testType, sep="_")
the character string "p.value.rankproduct"
"Rank product test"
the character string "Rank product test"
The p values returned are equivalent to the percentage of false prediction (pfp), which in theory is the equivalent of false discovery rate (FDR). It is possible that they are larger than 1.
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(RNAither)
Loading required package: topGO
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
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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: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
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groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
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Loading required package: RankProd
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Scalable Robust Estimators with High Breakdown Point (version 1.3-11)
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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAither/RankProduct.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RankProduct
> ### Title: Perform a Rank Product test
> ### Aliases: RankProduct
> ### Keywords: univar
>
> ### ** Examples
>
> data(exampleHeader, package="RNAither")
> data(exampleDataset, package="RNAither")
>
> pvals1 <- RankProduct(dataset, list(100, 1, "SigIntensity", "GeneName"))
Rank Product analysis for one-class case
Warning: There are 37 genes with at least one missing value.
This value is not used to compute rank product.
Starting 100 permutations...
Computing pfp ..
Outputing the results ..
> pValVec1 <- pvals1[[1]]
> scoredDataset1 <- pvals1[[2]]
>
>
>
>
>
> dev.off()
null device
1
>