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

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

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

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)
#> reading 55merge_omssa.mzid... DONE!
#> reading 55merge_tandem.mzid... DONE!

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