P-value adjusting function

Description

This function converts the given raw p-values into the FDR adjusted p-values using R package 'multtest'.

Usage

pvadjust(pvlist)

Arguments

Details

pvlist is the output from genediff containing p-values from gene-specific MSE's and posterior MSE's.

Value

Author(s)

David Rocke and Geun-Cheol Lee

References

David M. Rocke (2004), Design and analysis of experiments with high throughput biological assay data, Seminars in Cell & Developmental Biology, 15, 703-713.

http://www.idav.ucdavis.edu/~dmrocke/

See Also

genediff

Examples

#library
library(Biobase)
library(LMGene)

#data
data(sample.mat)
data(vlist)
LoggedSmpd0<-neweS(lnorm(log(sample.mat)),vlist)

pvlist<-genediff(LoggedSmpd0)
pvlist$Posterior[1:5,]

apvlist<-pvadjust(pvlist)
names(apvlist)
apvlist$Posterior.FDR[1:5,]

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.
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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(LMGene)
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: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

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

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LMGene/pvadjust.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pvadjust
> ### Title: P-value adjusting function
> ### Aliases: pvadjust
> ### Keywords: models
> 
> ### ** Examples
> 
> #library
> library(Biobase)
> library(LMGene)
> 
> #data
> data(sample.mat)
> data(vlist)
> LoggedSmpd0<-neweS(lnorm(log(sample.mat)),vlist)
> 
> pvlist<-genediff(LoggedSmpd0)
Prior d.f. =  5.565247 
Prior mean reciprocal precision =  0.02358122 
> pvlist$Posterior[1:5,]
          patient      dose
[1,] 3.876385e-01 0.3879211
[2,] 3.709678e-06 0.8022847
[3,] 2.528063e-09 0.5616116
[4,] 1.105484e-04 0.1437101
[5,] 3.448101e-03 0.2096670
> 
> apvlist<-pvadjust(pvlist)
> names(apvlist)
[1] "Gene.Specific"     "Posterior"         "Gene.Specific.FDR"
[4] "Posterior.FDR"    
> apvlist$Posterior.FDR[1:5,]
          patient      dose
[1,] 5.538984e-01 0.8926224
[2,] 2.274032e-04 0.9689393
[3,] 1.549703e-06 0.9331040
[4,] 2.420220e-03 0.8504015
[5,] 2.856332e-02 0.8504015
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>