PlotPTMAcrossSamples: Plot PTM across samples
In BioAlvaro/ProteoMS: Quality Control of Protemics Data

Description Usage Arguments Value Examples

Plot PTM across samples

PlotPTMAcrossSamples(
  MQCombined,
  PTM_of_interest = "Oxidation (M)",
  log_base = 2,
  long_names = FALSE,
  sep_names = NULL
)

`MQCombined`	Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`PTM_of_interest`	Post-Translation Modification of interest. It is important they are defined exactly as MaxQuant does: Examples: 'Oxidation (M)', 'Acetyl (Protein N-term)', 'Unmodified', etc.
`log_base`	The logarithmic scale for the intensity. Default is 2.
`long_names`	If TRUE, samples having long names will be considered, and the name will be split by sep_names. By default = FALSE.
`sep_names`	If long_names is TRUE, sep_names has to be selected. Samples names will be split. By default is NULL.

A plot showing the PTM of interest.

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MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
MQCombined <- make_MQCombined(MQPathCombined)
PlotPTMAcrossSamples(MQCombined, PTM_of_interest = 'Oxidation (M)')