PlotProteinCoverage: Protein coverage and degradation.
In BioAlvaro/MQmetrics: Quality Control of Protemics Data

Description Usage Arguments Value Examples

Protein coverage and degradation.

PlotProteinCoverage(
  MQCombined,
  UniprotID = NULL,
  log_base = 2,
  segment_width = 2,
  palette = "Set2",
  plots_per_page = 5
)

`MQCombined`	Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`UniprotID`	Uniprot ID of the protein of interest.
`log_base`	The logarithmic scale for the intensity. Default is 2.
`segment_width`	Width of the segments to improve visualization. Default is 1.
`palette`	The palette from the Package RColorBrewer. By default is 'Set2'.
`plots_per_page`	Establish the maximum number of plots per page.

Two plots for each sample, the end position vs the start position of each peptide of the given protein found. And the Intensity of a given peptide and its length.

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MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics')
MQCombined <- make_MQCombined(MQPathCombined)
PlotProteinCoverage(MQCombined, UniprotID = 'Q15149')