MrHedmad / fast-cohen

A fast implementation of a Cohen's D calculator

Fast Cohen's d calculator

A fast implementation of a Cohen's d calculator.

Installation

You will need cargo installed.

cargo install --git https://github.com/MrHedmad/fast-cohen.git

Usage

You will need two .csv files, each with the two sample groups. The first row of each input file should be the column names. The first column of each file should contain gene names (or generically any item name). The rest of the columns should be the data, and the order of these does not matter. The data should be numeric.

Then, simply call:

fast-cohen "control_samples" "case_samples" "output_csv"

You can use fast-cohen --help to see the help message:

Calculate cohen's d of expression values.

Usage: fast-cohen [OPTIONS] <CASE_EXPRESSION_MATRIX> <CONTROL_EXPRESSION_MATRIX> <OUTPUT_PATH>

Arguments:
  <CASE_EXPRESSION_MATRIX>     Path to the expression matrix with the 'case' expression matrix
  <CONTROL_EXPRESSION_MATRIX>  Path to the expression matrix with the 'control' expression matrix
  <OUTPUT_PATH>                Path and filename of the output file

Options:
  -d, --delimiter <DELIMITER>  Delimiter of the input files [default: "\t"]
  -h, --help  

The output csv will have a row_names column with the row names, and a cohen_d column with the Cohen's d values.

NOTE: The order of the samples in the two input files MUST be the same between the two input files. If you need to sort the rows, and the first column is the sample names, you can use xsv to sort the columns with the following command:

xsv sort "some_file" > "sorted_file"