GenRisk 0.0.7

Comprehensive genetic risk assessment

GenRisk

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

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 an annotated vcf (i.e: annotated with variant ID , ALT, Gene, and deleterious score, for more information check out the example in toy_example)

$ genrisk score-genes --annotated-vcf annotated_vcf_toy.vcf --temp-dir test/ --output-file test.tsv --weight-func beta --maf-threshold 0.01 --alt-col ALT --variant-col ID --af-col AF --del-col CADD --gene-col Gene

• 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 --scores-file toy_example/toy_dataset_scores --info-file toy_example/toy.pheno 
--cases-column trait1 --samples-column IID --test betareg --output-file toy_dataset_betareg.tsv --covariates age,sex
--adj-pval bonferroni

• For further CLI options and parameters use --help

Visualize

Visualize manhatten plot and qqplot for the data.

$ genrisk visualize --pvals-file toy_example/toy_dataset_scores --info-file annotated_toy_dataset.vcf
--qq-output toy_example/toy_dataset_qqplot.jpg --manhattan-output toy_example/toy_dataset_manhattanplot.jpg 

• For further CLI options and parameters use --help

Create model

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

$ genrisk create-model --data-file toy_example_regressor_features.tsv --model-type regressor --output-folder toy_regressor 
--test-size 0.25 --test --model-name toy_regressor --target-col trait1 --imbalanced --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: [e-mail]