Last data update: 2014.03.03

R: Perform a Rank Product test
RankProductR Documentation

Perform a Rank Product test

Description

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.

See Also

Ttest, MannWhitney

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

pvals1 <- RankProduct(dataset, list(100, 1, "SigIntensity", "GeneName"))
pValVec1 <- pvals1[[1]]
scoredDataset1 <- pvals1[[2]]

Results


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'

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: 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")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

Loading required package: RankProd
Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid

Attaching package: 'grid'

The following object is masked from 'package:topGO':

    depth

Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:Biobase':

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)


Attaching package: 'RNAither'

The following object is masked from 'package:IRanges':

    trim

> 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 
>