Display rate classification performance with thresholds visible at x-axis

Description

Display rate classification performance with thresholds visible at x-axis

A method to visualize the performance in the classification of synthesis, degradation and processing rates based on the comparison of the original simulated rates and the one obtained by the function modelRates. For each rate, classification performance is measured in terms of sensitivity and specificity using a ROC curve analysis. False negatives (FN) represent cases where the rate is identified as constant while it was simulated as varying. False positives (FP) represent cases where INSPEcT identified a rate as varying while it was simulated as constant. On the contrary, true positives (TP) and negatives (TN) are cases of correct classification of varying and constant rates, respectively. Consequently, at increasing brown p-values different sensitivity and specificity can be achieved.

Usage

rocThresholds(object, object2, cTsh = NULL, bTsh = NULL, xlim = c(1e-05,
  1))

## S4 method for signature 'INSPEcT_model,INSPEcT_model'
rocThresholds(object, object2,
  cTsh = NULL, bTsh = NULL, xlim = c(1e-05, 1))

## S4 method for signature 'INSPEcT_model,INSPEcT'
rocThresholds(object, object2, cTsh = NULL,
  bTsh = NULL, xlim = c(1e-05, 1))

Arguments

Value

None

See Also

makeSimModel, makeSimDataset, rocCurve

Examples

data('simRates', package='INSPEcT')
data('simData3rep', package='INSPEcT')
rocThresholds(simRates, simData3rep)
# Increase the Brown threshold for all rates (be more relaxed)
thresholds(simData3rep)$brown <- c(alpha=.05, beta=.05, gamma=.05)
rocThresholds(simRates, simData3rep)

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(INSPEcT)
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: BiocParallel
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/INSPEcT/rocThresholds.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rocThresholds
> ### Title: Display rate classification performance with thresholds visible
> ###   at x-axis
> ### Aliases: rocThresholds rocThresholds,INSPEcT_model,INSPEcT-method
> ###   rocThresholds,INSPEcT_model,INSPEcT_model-method
> 
> ### ** Examples
> 
> data('simRates', package='INSPEcT')
> data('simData3rep', package='INSPEcT')
> rocThresholds(simRates, simData3rep)
> # Increase the Brown threshold for all rates (be more relaxed)
> thresholds(simData3rep)$brown <- c(alpha=.05, beta=.05, gamma=.05)
Updating modeled rates...
> rocThresholds(simRates, simData3rep)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>