CI Adjust

Description

Multiple testing adjustment of confidence levels, as proposed by Benjamini and Yekutieli.

Usage

  ciAdjustLevel(eta0, conf_level)

Arguments

Value

The adjusted confidence level.

References

Benjamini, Yoav, and Daniel Yekutieli. False Discovery Rate<c3><a2><c2><80><c2><93>adjusted Multiple Confidence Intervals for Selected Parameters. Journal of the American Statistical Association 100, no. 469 (2005): 71<c3><a2><c2><80><c2><93>81.

Examples

conf_level = 0.95
eta0 = seq(0, 1, by = 0.02)

conf_level_adj = ciAdjustLevel(eta0, conf_level)

plot(eta0, conf_level_adj, pch = 20, ylim = c(conf_level, 1))

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(Rariant)
Loading required package: GenomicRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: SummarizedExperiment
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

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

    tabulate

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rariant/ci-adjust.rd_%03d_medium.png", width=480, height=480)
> ### Name: ciAdjust
> ### Title: CI Adjust
> ### Aliases: ciAdjustLevel
> 
> ### ** Examples
> 
> conf_level = 0.95
> eta0 = seq(0, 1, by = 0.02)
> 
> conf_level_adj = ciAdjustLevel(eta0, conf_level)
> 
> plot(eta0, conf_level_adj, pch = 20, ylim = c(conf_level, 1))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>