evalTargetDecoys {TargetDecoy} | R Documentation |
Create diagnostic plots to evaluate the TDA assumptions. A histogram and PP plot allow to check both necessary assumptions.
evalTargetDecoys(object, decoy, score, log10 = TRUE, nBins = 50) evalTargetDecoysPPPlot(object, decoy, score, log10 = TRUE, zoom = FALSE) evalTargetDecoysHist( object, decoy = NULL, score = NULL, log10 = NULL, nBins = 50, zoom = FALSE )
object |
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decoy |
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score |
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log10 |
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nBins |
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zoom |
Logical value indicating whether a zoomed version of the plot
should be returned. Default: |
evalTargetDecoys
returns an overview of the following four plots:
A PP plot showing the empirical cumulative distribution of the target distribution in function of that of the decoy distribution
A histogram showing the score distributions of the decoys and non-decoys
A zoomed PP plot
A zoomed histogram
evalTargetDecoysPPPlot
generates the PP plot only (1.) or the zoomed
version (3.) if zoom = TRUE
.
evalTargetDecoysHist
generates the histogram only (2.) or the zoomed
version (4.) if zoom = TRUE
.
Elke Debrie, Lieven Clement, Milan Malfait
library(mzID) ## Use one of the example files in the mzID package exampleFile <- system.file("extdata", "55merge_tandem.mzid", package = "mzID") mzIDexample <- mzID(exampleFile) # Plot the overview of the four plots evalTargetDecoys(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect", log10 = TRUE ) # Plot the PP plot only evalTargetDecoysPPPlot(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect", log10 = TRUE ) # Plot the zoomed PP plot only evalTargetDecoysPPPlot(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect", log10 = TRUE, zoom = TRUE ) # Plot the histogram only evalTargetDecoysHist(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect", log10 = TRUE ) # Plot the zoomed histogram only evalTargetDecoysHist(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect", log10 = TRUE, zoom = TRUE ) ## mzRident objects can also be used library(mzR) if (requireNamespace("msdata", quietly = TRUE)) { ## Using example file from msdata file <- system.file("mzid", "Tandem.mzid.gz", package = "msdata") mzid <- openIDfile(file) } evalTargetDecoys(mzid, decoy = "isDecoy", score = "X.Tandem.expect", log10 = TRUE )