Man pages for rivas-lab/snpnet
snpnet: Efficient Lasso Solver for Large SNP Data
| cat_or_zcat | select zstdcat, zcat, or cat |
| compose_regression_formula_str | Compose a regression formula give a response variable and the... |
| compute_matrix_product | Take a matrix product of data matrix (X_df) and coefficient... |
| config_params_data_type | This is a helper function for read_config_from_file(). Here,... |
| count_n_per_split | Count the number of individuals in each popluation split |
| eval_AUC_CI | Compute AUC with confidence interval. |
| eval_CI | Compute R-squared or AUC with confidence interval. |
| eval_r2_CI | Compute R-squared with confidence interval. |
| FID_IID_from_rownames | Recover FID and IID from rownames of the data frame |
| FID_IID_to_rownames | Assign rownames of phenotype data frame based on FID and IID |
| fit_glm | A wrapper function for glm() |
| fit_glm_across_splits | Fit a specified regression model for each split independently... |
| fit_to_df | convert the fit object to a data frame |
| get_ID_ALTs | Get ID_ALT of genetic variants |
| glm_fit_to_r2 | Get r-squared value from glm fit object |
| parse_covariates | Parse a string containing the set of covariates. |
| plot_PRS_binomial | generate Violin plot comparing the distribution of PRSs... |
| plot_PRS_vs_phe | generate a 2d heatmap plot comparing the PRS (Z-score if... |
| predict_snpnet | Predict from the Fitted Object or File |
| read_config_from_file | Read a configuration from a file |
| read_lambda_sequence_from_RData_file | Load a lambda sequence from a R Data file |
| readPheMaster | Read covariates and phenotype(s) from the provided file path |
| read_phenotype_file | Read a phenotype file as a data frame |
| read_sscore_file | Read a PRS file as a data frame |
| recode_pheno_values | Recode phenotype values |
| save_BETA | save the regression coefficients (betas) into file(s). |
| snpnet | Fit the Lasso/Elastic-Net for Large Phenotype-Genotype... |
| snpnet_fit_to_df | convert the snpnet regression coeffieicnets (betas) into a... |
| split_list_str | split a list string into a list |
| split_named_list_str | split a list string into a named list |
| update_split_column_for_refit | Collapse the training (train) and validation (val) sets into... |
