createReport: Create a quality control report (in PDF format).

Description Usage Arguments Details Value Note

View source: R/fcn_computeQC.R

Description

This is the main function of the package and the only thing you need to call directly if you are just interested in getting a QC report.

Usage

1
createReport(txt_folder, yaml_obj = list(), report_filenames = NULL)

Arguments

txt_folder

Path to txt output folder of MaxQuant (e.g. "c:/data/Hek293/txt")

yaml_obj

A nested list object with configuration parameters for the report. Useful to switch off certain plots or skip entire sections.

report_filenames

Optional list with names (as generated by getReportFilenames). If not provided, will be created internally by calling getReportFilenames.

Details

You need to provide the folder name of the 'txt' output, as generated by MaxQuant and optionally a YAML configuration object, which allows to (de)activate certain plots and holds other parameters. The yaml_obj is complex and best obtained by running this function once using the default (empty list). A full YAML configuration object will be written in the 'txt' folder you provide and can be loaded using yaml.load.

The PDF and the config file will be stored in the given txt folder.

Value

List with named filename strings, e.g. $yaml_file, $report_file etc..

Note

You need write access to the txt folder!

For updates, bug fixes and feedback please visit http://github.com/cbielow/PTXQC.


PTXQC documentation built on Feb. 9, 2018, 6:08 a.m.