README.md

In davidsbutcher/CRawFISh: Create summary info from a tdReport or directory of Thermo Raw files.

CRawFISh

Make a statistical summary sheet for any number of Thermo raw files generated by Thermo FT instruments. This package utilizes the program rawDiag to extract data from raw files. rawDiag must be installed and all system requirements listed on the rawDiag site must be met.

Installation

Install from GitHub:

remotes::install_github("davidsbutcher/crawfish")

Usage

The exported function from this package, crawfish, can be used to get summary information on raw files. Raw files can be specified by providing a directory or a tdReport file generated by TDPortal analysis.

Directory

crawfish(
      rawFileDir = "C:/rawfiles/experiment1",
      outputDir = "C:/rawfiles/experiment1_output"
   )

All .raw files in rawFileDir and its subdirectories will be read and summarized.

tdReport

crawfish(
      rawFileDir = "C:/rawfiles/experiment1",
      use_tdreport = TRUE,
      tdReportDir = "C:/tdreports",
      tdReportName = "201912_experiment1.tdReport",
      outputDir = "C:/rawfiles/experiment1_output"
   )

rawFileDir will be searched for the file called tdReportName. If found, names of all raw files which were searched to generate the report are extracted. The rawFileDir is then searched for the extracted raw files, which are read and summarized as above. Note that the names of the raw files in the tdReport must match the names of the files in the rawFileDir.

Additional arguments

For all analyses, the following arguments can be specified:

• maxinjectcutoff: Fraction of maximum injection time that is used to determine the cutoff for “max injects”. Defaults to 0.99.

• make_report: Boolean value (TRUE or FALSE). Determines whether an HTML report is generated in the outputDir. Defaults to TRUE.

• export_raw_info: Boolean value (TRUE or FALSE). Controls whether an output file is generated containing all extracted metadata without summarization. This file can be quite large. Defaults to FALSE.

Dependencies

This package imports assertthat, ggplot2, rawDiag and selected functions from RSQLite, dplyr, fs, magrittr, openxlsx, purrr, rmarkdown, stringr, and tibble.

License and attribution

This package utilizes the program rawDiag to extract data from raw files. rawDiag is licensed under GNU GPL v3.0.

All other components are written by David S. Butcher and available under an MIT license.

davidsbutcher/CRawFISh documentation built on July 7, 2021, 1:03 p.m.