generateReport: Generates a report including all the plots of MQmetrics.

Description Usage Arguments Value Examples

View source: R/generateReport.R

Description

Generates a report including all the plots of MQmetrics.

Usage

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generateReport(
  MQPathCombined,
  output_dir = getwd(),
  name_output_file = "MQmetrics_report.pdf",
  remove_contaminants = TRUE,
  log_base = 2,
  long_names = FALSE,
  sep_names = NULL,
  intensity_type = "Intensity",
  palette = "Set2",
  UniprotID = NULL,
  segment_width = 1,
  show_shade = TRUE,
  percent_proteins = 0.9,
  show_calibrated_rt = FALSE,
  tolerance = 0.001,
  show_max_value = TRUE,
  peptides_modified = 1,
  show_median = TRUE,
  size_median = 1.5,
  binwidth = 0.1,
  plot_unmodified_peptides = FALSE,
  aggregate_PTMs = TRUE,
  combine_same_residue_ptms = TRUE,
  PTM_of_interest = "Oxidation (M)",
  plots_per_page = 5
)

Arguments

MQPathCombined

The directory to the "combined" folder where the MaxQuant results are stored.

output_dir

The directory where the results will be stored. By default is the working directory.

name_output_file

The name of the report generated.

remove_contaminants

Whether or not to remove contaminants, reverse and identified by one one peptide.

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.

intensity_type

The type of intensity of interest. Values: 'Intensity' or 'LFQ'. Default = 'Intensity'.

palette

The palette from the Package RColorBrewer. By default is 'Set2'.

UniprotID

Uniprot ID of the protein of interest. PlotProteinCoverage().

segment_width

Width of the segments to improve visualization. Default is 1. (PlotProteinCoverage).

show_shade

Creates a shade showing where the percent_proteins are. Default is TRUE. PlotAllDynamicRange(), PlotCombinedDynamicRange().

percent_proteins

Determines the percentage for the show_shade parameter. Default is 0.90 (90% of the proteins). PlotAllDynamicRange(), PlotCombinedDynamicRange().

show_calibrated_rt

If TRUE, it will also show the calibrated retention time of each iRT peptide. By default = FALSE. PlotiRT().

tolerance

Error maximum to find the iRT peptides by m/z value. By default is 0.001.

show_max_value

If TRUE, it will show the max TIC value of each sample. PlotTotalIonCurrent().

peptides_modified

Minimum number of peptides modified. Default is 5. PlotPTM().

show_median

If true it will show the median of each group, as a red dashed line.By default is TRUE. PlotHydrophobicity().

size_median

The width of the median line in the plots.

binwidth

Selects the binwidth of the histogram. By default = 0.2. PlotHydrophobicity().

plot_unmodified_peptides

If TRUE, it will show the Unmodified peptides. PlotPTM().

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).

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.

plots_per_page

Establish the maximum number of plots per page.

Value

A pdf document with all the results of MQmetrics package.

Examples

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## Not run: 
MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics')
generateReport(MQPathCombined)

## End(Not run)

BioAlvaro/MQviewer documentation built on Jan. 11, 2022, 8:25 p.m.