Accessor and setter for the 'FDRresults' slot of a DChIPRepResults object.

Description

The slot contains the results of the FDR estimation as performed within the function runTesting. It is the complete output of the fdrtool function.

Usage

## S4 method for signature 'DChIPRepResults'
FDRresults(object)

## S4 replacement method for signature 'DChIPRepResults,list'
FDRresults(object) <- value

Arguments

Value

a list containing the estimated false discovery rates

Examples

data(testData)
dcr <- DChIPRepResults(testData)
dcr <- runTesting(dcr)
str(FDRresults(dcr))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(DChIPRep)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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")'.


Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DChIPRep/FDRresults.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FDRresults
> ### Title: Accessor and setter for the 'FDRresults' slot of a
> ###   'DChIPRepResults' object.
> ### Aliases: FDRresults FDRresults,DChIPRepResults-method FDRresults<-
> ###   FDRresults<-,DChIPRepResults,list-method
> 
> ### ** Examples
> 
> data(testData)
> dcr <- DChIPRepResults(testData)
> dcr <- runTesting(dcr)
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr

> str(FDRresults(dcr))
List of 5
 $ pval     : num [1:2500] 1 1 0.93 1 0.155 ...
 $ qval     : num [1:2500] 0.919 0.919 0.913 0.919 0.637 ...
 $ lfdr     : num [1:2500] 1 1 1 1 1 1 1 1 1 1 ...
 $ statistic: chr "pvalue"
 $ param    : num [1, 1:4] 1.12e-01 2.04e+03 9.19e-01 8.72e-03
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:4] "cutoff" "N.cens" "eta0" "eta0.SE"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>