evalTargetDecoys {TargetDecoy}

R Documentation

Evaluate assumptions of the Target Decoys approach

Description

Create diagnostic plots to evaluate the TDA assumptions. A histogram and PP plot allow to check both necessary assumptions.

Usage

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
)

Arguments

object	A data.frame, mzID or mzRident object.
decoy	character, name of the variable that indicates if the peptide matches to a target or to a decoy.
score	numeric, indicating the score of the peptide match, obtained by the search engine.
log10	logical to indicate if the score should be -log10-transformed.
nBins	numeric indicating the number of bins in the histogram.
zoom	Logical value indicating whether a zoomed version of the plot should be returned. Default: FALSE.

Value

evalTargetDecoys returns an overview of the following four plots:

1. A PP plot showing the empirical cumulative distribution of the target distribution in function of that of the decoy distribution

2. A histogram showing the score distributions of the decoys and non-decoys

3. A zoomed PP plot

4. 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.

Author(s)

Elke Debrie, Lieven Clement, Milan Malfait

Examples

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
)

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