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

In BioAlvaro/MQmetrics: Quality Control of Protemics Data

Description

Generates a report including all the plots of MQmetrics.

Usage

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

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

## End(Not run)

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