PlotPTMAcrossSamples: Plot PTM across samples

Description Usage Arguments Value Examples

View source: R/PlotPTMAcrossSamples.R

Description

Plot PTM across samples

Usage

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

Arguments

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.

Value

A plot showing the PTM of interest.

Examples

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

svalvaro/MQmetrics documentation built on Jan. 14, 2022, 6:36 p.m.