Overview

The Crosstab Merger combines crosstab files (aka PivotTables) that have a similar format, creating a single merged crosstab file.

Downloads

Download a .zip file with the program from: https://github.com/PNNL-Comp-Mass-Spec/Crosstab-Merger/releases

Example Data Files

Browse example input and output files at
https://github.com/PNNL-Comp-Mass-Spec/Crosstab-Merger/tree/master/Docs

Console Switches

The CrossTab Merger is a command line application.
Syntax:

CrosstabMerger.exe
 /I:InputFilePathSpec [/O:OutputFileNameOrPath]
 [/D:OutputDirectory] [/Y]
 [/H:HeaderRowCount] [/K:KeyColumnCount] [/Preview]
 [/Conf:KeyValueParamFilePath] [/CreateParamFile] 

Use /I to specify the pattern to use to find files to merge

• The name must contain a wildcard character (either * or ?) so that multiple files can be found
• For example, use Block*.csv to match all CSV files that start with "Block"
• Or, use Block?_RelativeAbundanceRatios.csv to match these four CSV files at https://github.com/PNNL-Comp-Mass-Spec/Crosstab-Merger/tree/master/Docs
  • Block1_RelativeAbundanceRatios.csv
  • Block2_RelativeAbundanceRatios.csv
  • Block3_RelativeAbundanceRatios.csv
  • Block4_RelativeAbundanceRatios.csv

The output file name is optional, but can be specified using /O

• For example, /O:MergedAbundanceRatios.csv
• If omitted, the output file will be auto-named, based on InputFilePathSpec

Use /D to specify the output directory

Use /Y to allow overwriting an existing output file

Use /H to specify the number of header rows

• By default, the program assumes just one header row
• For example, the PeptideQuantitation tab-delimited text files on GitHub at https://github.com/PNNL-Comp-Mass-Spec/Crosstab-Merger/tree/master/Docs have one header row (and one key column)
  • The RelativeAbundanceRatios CSV files on GitHub have three header rows (and two key columns)

Use /K to specify the number of key columns

• This is the number of columns that provide metadata about the crosstab data
  • If the crosstab has peptide quantitation values, and the data file lists protein name in the first column and peptide sequence in the second column, the file has two key columns
• As mentioned for /H, the PeptideQuantitation text files on GitHub have one key column
  • The RelativeAbundanceRatios CSV files on GitHub have two key columns

Use /Preview to read the input files and see the number of datasets found and rows that would be written

Use /P or /Conf to define a key/value parameter file with settings to load

• Example Key=Value parameter files
  • MergerOptions_OneHeaderRow_OneKeyColumn.txt
  • MergerOptions_ThreeHeaderRows_TwoKeyColumns.txt

Contacts

Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics

License

Crosstab Merger is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2020 Battelle Memorial Institute