generateReport {MQmetrics} | R Documentation

## Generates a report including all the plots of MQmetrics.

### 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)

[Package MQmetrics version 1.2.0 Index]