Find the bound.cutoff

Description

Define the bound.cutoff using either the normalNull or the twoGaussiansNull method.

Usage

  findBoundCutoff(xSet, method = c("normalNull", "twoGaussiansNull"), mean.method = "mode", 
    pvalue = FALSE, fdr = FALSE, pvalPlot = FALSE)

Arguments

Details

We implemented two methods to set the bound.cutoff, probes above this threshold are considered “bound”. The twoGaussiansNull method established in the Ringo package (Toedling et al., 2007), by which the data is assumed to follow a mixture of two Gaussian distributions. The one Gaussian with the lower mean value is assumed to be the null distribution and probe levels are assigned p-values based on this null distribution. Alternatively the user can select the normalNull method instead which assumes the null distribution is normal and symmetrical around the mode (or zero). For both methods the user can decide if the resulting p-values are to be adjusted for multiple testing (fdr) or selected by a p-value threshold. The function also provides QC plots for the twoGaussiansNull and an optional p-value histogram.

Value

Returns a numeric

Note

Please note that the use of the package “mclust” is only free for strict academic use (see the license of “mclust” here: http://www.stat.washington.edu/mclust/license.txt). The alternative function normalNull does not have this restriction.

Author(s)

Bettina Fischer

References

Toedling J., Skylar O., Krueger T, Fischer J.J., Sperling S., Huber W. 2007 Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics, 8:221

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  bound.cutoff <- findBoundCutoff(SGR, method="twoGaussiansNull", fdr=0.25)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(SimBindProfiles)
Loading required package: Ringo
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: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SimBindProfiles/findBoundCutoff.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findBoundCutoff
> ### Title: Find the bound.cutoff
> ### Aliases: findBoundCutoff
> 
> ### ** Examples
> 
>   dataPath <- system.file("data",package="SimBindProfiles")
>   load(file.path(dataPath,"SGR.RData"))
>   bound.cutoff <- findBoundCutoff(SGR, method="twoGaussiansNull", fdr=0.25)
Using bound.cutoff = 2.05 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>