tumordeconv/imputation repository overview

⁠Proteomic data imputation

This module leverages the imputation algorithm developed during the NCI-CPTAC DREAM Proteogenomics Challenge⁠. The resulting DreamAI algorithm imputes missing values in proteomics data given observed proteins.

⁠Usage

This tool can be run from the command-line with the CWL tool file and an input YAML file:

cwl-runner imputation-tool.cwl imputation-input.yml 

This tool can also be run with a cwl engine without an input file as follows:

cwl-runner imputation-tool.cwl --input_f test-data.tsv --use_missForest false

This will output an imputed_file.tsv containing a tab-separated matrix of imputed protein values in the CWL tool's working directory.

⁠Inputs

The imputation.yml file can be updated with custom inputs.

The included example file uses test dummy data in this directory:

imputation-input.yml

input_f:
  class: File
  path: test-data.csv

use_missForest: 'false'

This module requires two inputs: