sickle-in-africa/newborn-screening

a repository for the Newborn screening study # Newborn Screening Study Code: HPLC and POCT This repository contains R code for performing analyses related to the SickleInAfrica **Newborn Screening Study**. The study evaluates the accuracy of POCT (Point-of-Care Testing) compared to the gold standard HPLC/IEF method across different sites. The code calculates key performance metrics, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). --- ## Repository Structure - **`HPLC/`**: Contains code for performance calculations, with HPLC/IEF as the gold standard. - **`POCT/`**: Contains code for performance calculations, with POCT as the gold standard. - **`Quantitative/`**: Contains scripts and outputs for the quantitative analysis phase, focusing on large-scale data integration and statistical modeling. --- ## Purpose This repository supports the full lifecycle of newborn screening data analysis: - Ensuring **data integrity and completeness** - Performing **imputation for missing values** - Conducting **quality control and diagnostics** - Enabling **statistical analysis by genotype** - Producing **reproducible outputs and reports** - Extending into a **quantitative phase** for pooled, multi-country analyses --- ## Key Metrics The following performance metrics are calculated as part of the study: 1. **Sensitivity**: Proportion of true positives correctly identified by DBS/POCT. 2. **Specificity**: Proportion of true negatives correctly identified by DBS/POCT. 3. **Positive Predictive Value (PPV)**: Proportion of positive results by DBS/POCT that are true positives. 4. **Negative Predictive Value (NPV)**: Proportion of negative results by DBS/POCT that are true negatives. 5. **Quantitative Measures** (new phase): Cross-site pooled performance estimates, confidence intervals, heterogeneity tests, and regression-based modeling. --- ## Data Requirements - **Input Data**: - Screening results for both HPLC and POCT. - Quantitative data aggregated across site …