README.md

In twillis209/pidProjCode: Utility code for my work on primary immunodeficiency

Toy R package written to make available some project-specific utility code and to help me learn to create packages

The karyoploteR vignette uses data from four GWAS: 1. 'Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency', Bronson et al. (2016), https://doi.org/10.1038/ng.3675 2. 'Whole-genome sequencing of a sporadic primary immunodeficiency cohort', Thaventhiran et al. (2020), https://doi.org/10.1038/s41586-020-2265-1 3. 'Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus', Bentham et al. (2015), https://doi.org/10.1038/ng.3434 4. 'Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease', de Lange et al. (2017), https://doi.org/10.1038/ng.3760

Summary statistics for each of these can be downloaded from the EBI GWAS Catalog. The summary statistics included in the package were processed using the GWAS_tools pipeline by my colleague Dr Guillermo Reales, who developed the tool.

twillis209/pidProjCode documentation built on Nov. 7, 2021, 3:01 p.m.