PlotPTM: Post-Translational Modifications

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

Description

Post-Translational Modifications

Usage

PlotPTM(
  MQCombined,
  peptides_modified = 1,
  plot_unmodified_peptides = FALSE,
  log_base = 2,
  aggregate_PTMs = TRUE,
  combine_same_residue_ptms = TRUE,
  palette = "Set2",
  plots_per_page = 5
)

Arguments

MQCombined	Object list containing all the files from the MaxQuant output. It is the result from using make_MQCombined.
peptides_modified	Minimum number of peptides modified. Default is 5.
plot_unmodified_peptides	If TRUE, it will show the Unmodified peptides.
log_base	The logarithmic scale for the intensity. Default is 2.
aggregate_PTMs	If TRUE, same PTM that occur multiple times in the same peptides, will be aggregated together.
combine_same_residue_ptms	Combine the PTMs that happen in the same residue such as Dimethyl (KR), Trimethyl (KR) into only one group: Methyl (KR).
palette	The palette from the Package RColorBrewer. By default is 'Set2'.
plots_per_page	Establish the maximum number of plots per page.

Value

Two plots per sample

Examples

MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
MQCombined <- make_MQCombined(MQPathCombined)
PlotPTM(MQCombined)

BioAlvaro/MQmetrics documentation built on Jan. 12, 2022, 3:02 p.m.