createPPlotObjects {TargetDecoy} | R Documentation

## Create all the PP plots in one figure for scores from multiple objects

### Description

Create all the PP plots in one figure for scores from multiple objects

### Usage

    createPPlotObjects(object_list, decoy, score, log10 = TRUE)

### Arguments

`object_list` | List of mzID or mzRident objects. If named, the names will be used in the legend of the plot. If not, names will be extracted from the data files in case of mzID or mzRident objects.
`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.

### 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 two example files from the mzID package
    exampleFiles <- system.file(
        "extdata", c("55merge_omssa.mzid", "55merge_tandem.mzid"),
        package = "mzID"
    )
    mzObjects <- lapply(exampleFiles, mzID)

    createPPlotObjects(mzObjects,
        decoy = "isdecoy",
        score = c("omssa:evalue", "x\\!tandem:expect"),
        log10 = TRUE
    )

[Package TargetDecoy version 1.0.0 Index]