createPPlotObjects: Create all the PP plots in one figure for scores from...

In statOmics/TargetDecoy: Diagnostic Plots to Evaluate the Target Decoy Approach

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. When this value is missing, a Shiny gadget is launched to select it interactively.
score	numeric, indicating the score of the peptide match, obtained by the search engine. When this value is missing, a Shiny gadget is launched to select it interactively.
log10	logical to indicate if the score should be -log10-transformed. Default: TRUE. When this value is missing, a Shiny gadget is launched to select it interactively.

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
)

statOmics/TargetDecoy documentation built on Nov. 9, 2022, 9:30 a.m.