GenRisk

GenRisk is a package that implements different gene-based scoring schemes to analyze and find significant genes within a phenotype in a population

Citation

Rana Aldisi, Emadeldin Hassanin, Sugirthan Sivalingam, Andreas Buness, Hannah Klinkhammer, Andreas Mayr, Holger Fröhlich, Peter Krawitz, Carlo Maj, GenRisk: a tool for comprehensive genetic risk modeling, Bioinformatics, Volume 38, Issue 9, 1 May 2022, Pages 2651–2653, https://doi.org/10.1093/bioinformatics/btac152

Requirements

• plink >= 1.9 https://www.cog-genomics.org/plink/
• R version >= 3.6.3

Installation

Option 1: The latest release of GenRisk can be installed on python3+ with:

$ pip install genrisk

Option2: you can also install the package with the latest updates directly from GitHub <https://github.com/AldisiRana/GenRisk>_ with:

$ pip install git+https://github.com/AldisiRana/GenRisk.git

Usage

Score genes

This command calculate the gene-based scores for a given dataset.

It requires plink binary files, and an annotations file that contains all information needed for the score computation.

$ genrisk score-genes -a ../toy_example/toy_annotations.tsv -b ../toy_example/toy_data.bim -o toy_genes_scores_test_mod.tsv -t toy_vcf_scoring -v SNP -f gnomadAF -g gene -l ALT -d CADD_raw 

• For further CLI options and parameters use --help

Calculate p-values

This function calculates the p-values across the genes between two given groups

$ genrisk find-association -s toy_genes_scores.tsv -i info.pheno -t linear -c quan -a fdr_bh -v sex,age,bmi 

• For further CLI options and parameters use --help

Visualize

Visualize manhatten plot and qqplot for the data.

$ genrisk visualize -p logit_assoc_binary.tsv -i genes_info_ref.txt --genescol-1 genes

• For further CLI options and parameters use --help

Create model

Create a prediction model (classifier or regressor) with given dataset

$ genrisk create-model -d toy_dataset_feats.tsv -o quan_regression_model -n quan_regression_model --model-type regressor -l quan --normalize

• For further CLI options and parameters use --help

Test model

Evaluate a prediction model with a given dataset.

$ genrisk test-model --model-path regressor_model.pkl --input-file testing_dataset.tsv --model-type regressor 
--labels-col target --samples-col IID

• For further CLI options and parameters use --help

Get PRS scores

This command aquires a PGS file (provided by the user or downloaded from pgscatalog) then calculates the PRS scores for dataset. Note: This command is interactive.

$ genrisk get-prs

• For further CLI options and parameters use --help

Get GBRS

Calculate gene-based risk scores for individuals. If users do not have weights for calculation, they can provide a file with the phenotype and weights will be calculated.

$genrisk get-gbrs --scores-file scores_file.tsv --weights-file weights_file.tsv --weights-col zscore --sum

• For further CLI options and parameters use --help

Contact

If you have any questions or problems with the tool or its installation please feel free to create an issue in the repository or contact me via email: aldisi.rana@gmail.com