generateReport {MQmetrics} | R Documentation |
Generates a report including all the plots of MQmetrics.
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, plots_per_page = 5 )
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.
|
segment_width |
Width of the segments to improve visualization. Default is 1. (PlotProteinCoverage). |
show_shade |
Creates a shade showing where the |
percent_proteins |
Determines the percentage for the show_shade
parameter. Default is 0.90 (90% of the proteins).
|
show_calibrated_rt |
If TRUE, it will also show the calibrated
retention time of each iRT peptide. By default = FALSE. |
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.
|
peptides_modified |
Minimum number of peptides modified. Default is 5.
|
show_median |
If true it will show the median of each group, as a red
dashed line.By default is TRUE. |
size_median |
The width of the median line in the plots. |
binwidth |
Selects the binwidth of the histogram. By default = 0.2.
|
plot_unmodified_peptides |
If TRUE, it will show the Unmodified
peptides. |
plots_per_page |
Establish the maximum number of plots per page. |
A pdf document with all the results of MQmetrics package.
## Not run: MQPathCombined <- system.file('extdata/combined/', package = 'MQmetrics') generateReport(MQPathCombined) ## End(Not run)