createPPlotScores {TargetDecoy} | R Documentation

## Evaluate assumptions of the Target Decoys Approach for multiple search engines

### Description

Create diagnostic PP plots in one figure to evaluate the TDA assumptions for multiple search engines. The function provides the possibility to evaluate each of the sub-engines and the overall itself.

### Usage

    createPPlotScores(object, scores, decoy, log10 = TRUE)

### Arguments

`object` | A `data.frame`, mzID or mzRident object.
`scores` | A `character` vector of multiple score names from the input object. Typically from different search engines.
`decoy` | `character`, name of the variable that indicates if the peptide matches to a target or to a decoy.
`log10` | `logical` to indicate if the score should be `-log10`-transformed.

### Value

One PP plot with all original pi0, and a standardized / rescaled PP plot with all `pi0` set to 0.

### Author(s)

Elke Debrie, Lieven Clement

### 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)

    plots <- createPPlotScores(mzIDexample,
        scores = c("x\\!tandem:hyperscore", "x\\!tandem:expect"),
        decoy = "isdecoy", log10 = TRUE
    )

[Package TargetDecoy version 1.0.0 Index]