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Last data update: 2014.03.03

R: Function to calculate the sLA test statistic for a given...

getsLA-methods

R Documentation

Function to calculate the sLA test statistic for a given triplet data

Description

'getsLA' is used to calculate the sLA test statistic and correponding p value.

Arguments

`object`	An numerical matrix object with three columns or an object of ExpresionSet class with three features.
`boots`	The number of bootstrap iterations for estimating the bootstrap standard error of sGLA. Default value is boots=30.
`perm`	The number of permutation iterations for generating the null distribution of the sGLA test statistic. Default is perm=100.
`dim`	An index of the column for the gene to be treated as the third controller variable. Default is dim=3
`geneMap`	A character vector with three elements representing the mapping between gene names and feature names (optional).

Details

The input object can be a numerical matrix with three columns with row representing observations and column representing three variables. It can also be an ExpressionSet object with three features. If input a matrix class data, all three columns of the object representing the variables should have column names. Each variable in the object will be standardized with mean 0 and variance 1 in the function. In addition, the third variable will be quantile normalized within the function. More detail example about the usage of geneMap is demonstrated in the vignette.

Value

'getsLA' returns a vector with two elements. The first element is the value of test statistic and second element is the corresponding p value. A more detailed interpretation of these values is illustrated in the vignette.

Examples

data<-matrix(rnorm(300), ncol=3)

colnames(data)<-c("Gene1", "Gene2", "Gene3")

sLAest<-getsLA(data, boots=20, perm=100)

sLAest

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(LiquidAssociation)
Loading required package: geepack
Loading required package: yeastCC
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: org.Sc.sgd.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LiquidAssociation/getsLA-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getsLA-methods
> ### Title: Function to calculate the sLA test statistic for a given triplet
> ###   data
> ### Aliases: getsLA-methods getsLA,eSet-method getsLA,matrix-method getsLA
> ### Keywords: methods htest
> 
> ### ** Examples
> 
> data<-matrix(rnorm(300), ncol=3)
> 
> colnames(data)<-c("Gene1", "Gene2", "Gene3")
> 
> sLAest<-getsLA(data, boots=20, perm=100)
> 
> sLAest
      sLA   p value 
0.2199414 0.8200000 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>