The following functionality is offered for the 450K and EPIC chips:
- Screen for problematic samples, e.g. failed assays, mislabeled or contaminated samples (
control_metrics, check_sex, snp_outliers). - Compute detection p-values and mask respective data points (
detectionP, mask). - Preprocess the data (
correct_dye_bias, dont_normalize). - Estimate leukocyte composition in case of blood samples (
estimateLC)
Read the vignette on the recommended QC workflow at https://hhhh5.github.io/ewastools/articles/exemplary_ewas.html.
Package documentation is available at https://hhhh5.github.io/ewastools/.
An open access paper describing the quality checks implemented in this package in detail is available at http://doi.org/10.1186/s13148-018-0504-1. A vignette demonstrating the application of quality control checks on a public dataset is provided as well.
A second paper (open access) describing the improved detection p-values implemented in ewastools can be found at https://doi.org/10.1186/s13148-019-0615-3.
For installation please run devtools::install_github("hhhh5/ewastools")