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Last data update: 2014.03.03

R: Calculate bootstrap p-values for correlation measures

bootstrapCor

R Documentation

Calculate bootstrap p-values for correlation measures

Description

This function takes a numerical matrix (or two vectors) and calculates bootstrapped (by permutation) p-values to test if the correlation value is equal to zero. If the first argument is a matrix, the p-values are calculated between all pairs of rows of the matrix.

Usage

bootstrapCor(x, y=NULL, bRep, type="Rpearson", ret="p-value",
             alternative="two.sided")

Arguments

`x`	numerical matrix or vector to be analysed. If a vector, the argument `y` must be informed.
`y`	numerical vector. Must be informed if `x` is a vector. If `x` is a matrix, this argument is ignored. Defaults to NULL.
`bRep`	number of permutation to be done in the test.
`type`	character string specifying the type of correlation statistic to be used. Possible values are 'Rpearson', 'pearson', 'spearman' or 'kendall'.
`ret`	character string with the value to return. Must be 'p-value' (default) for the usual p-value or 'max', to return the maximum absolute correlation value obtained by the permutation.
`alternative`	character specifying the type of test to do, must be 'two.sided' (default), 'less' or 'greater'.

Details

Pearson, spearman and kendall types of correlation values are calculated by cor function from package stats. The method Rpearson was developed in this package and is a generalisation of the jackniffe correlation proposed by Heyer et al. (1999), it is calculated using the function robustCorr.

Value

The result of this function is a square matrix (length equal to the number of rows of x) if x is a matrix or a numerical value if x and y are vectors. The result is the p-values or maximum correlation values calculated by permutation tests.

Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

References

Heyer, L.J.; Kruglyak, S. and Yooseph, S. Exploring expression data: identification and analysis of coexpressed genes, Genome Research, 9, 1106-1115, 1999 (http://www.genome.org/cgi/content/full/9/11/1106)

Examples

x <- runif(50, 0, 1)
y <- rbeta(50, 1, 2)
bootstrapCor(x, y, bRep=100)

z <- matrix(rnorm(100, 0, 1), 4, 25)
bootstrapCor(z, bRep=100)

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(maigesPack)
Loading required package: convert
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/bootstrapCor.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bootstrapCor
> ### Title: Calculate bootstrap p-values for correlation measures
> ### Aliases: bootstrapCor
> ### Keywords: methods
> 
> ### ** Examples
> 
> x <- runif(50, 0, 1)
> y <- rbeta(50, 1, 2)
> bootstrapCor(x, y, bRep=100)
[1] 0.2
> 
> z <- matrix(rnorm(100, 0, 1), 4, 25)
> bootstrapCor(z, bRep=100)
     [,1] [,2] [,3] [,4]
[1,] 1.00 0.62 0.29 0.06
[2,] 0.62 1.00 0.73 0.75
[3,] 0.29 0.73 1.00 0.16
[4,] 0.06 0.75 0.16 1.00
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>