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

Description

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/`.

Usage

getReportFilenames(
  folder,
  report_name_has_folder = TRUE,
  mzTab_filename = NULL
)

Value

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**

Arguments

folder: Directory where the MaxQuant output (txt folder) or the mzTab file resides
report_name_has_folder: 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/`)
mzTab_filename: 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.