getReportFilenames: Assembles a list of output file names, which will be created...

View source: R/fcn_misc.R

getReportFilenamesR Documentation

Assembles a list of output file names, which will be created during reporting.


You can combine **report_name_has_folder** (and **mzTab_filename** for mzTab files) to obtain report filenames which are even more robust to moving around (since they contain infixes of the mzTab filename and the folder), e.g. '@em 'report_HEK293-study_myProjects.html“, where the input was ‘mzTab_filename=’HEK293-study.mzTab‘ and 'folder=’c:/somePath/myProjects/'.


  report_name_has_folder = TRUE,
  mzTab_filename = NULL



Directory where the MaxQuant output (txt folder) or the mzTab file resides


Boolean: Should the report files (html, pdf) contain the name of the deepest(=last) subdirectory in **txt_folder** which is not 'txt'? Useful for discerning different reports in a PDF viewer. E.g. when flag is FALSE: 'report_v0.91.0.html'; and 'report_v0.91.0_bloodStudy.html' when flag is TRUE (and the txt folder is '.../bloodStudy/txt/' or '...bloodStudy/')


If input is an mzTab, specify its name, so that the filenames can use its basename as infix E.g. when ‘mzTab_filename = ’HEK293-study.mzTab'' then the output will be 'report_HEK293-study.html'. This allows to get reports on multiple mzTabs in the same folder without overwriting report results.


List of output file names (just names, no file is created) with list entries: **yaml_file**, **heatmap_values_file**, **R_plots_file**, **filename_sorting**, **mzQC_file**, **log_file**, **report_file_prefix**, **report_file_PDF**, **report_file_HTML**

PTXQC documentation built on March 22, 2022, 5:08 p.m.