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

In cbielow/PTXQC: Quality Report Generation for MaxQuant and mzTab Results

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
)

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.

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**

cbielow/PTXQC documentation built on March 13, 2024, 5:08 a.m.