This repo was an early proof of concept, a more mature approach is available from Martin Morgan.
This package provides elementary interfaces to AlphaMissense resources, using BiocFileCache, Rsamtools, and GenomicRanges. But the AlphaMissense package is much more developed, please use it.
Installation at this time:
BiocManager::install("vjcitn/BiocAlphaMissense")
The vignette reviews how to use the gene-level summaries of pathogenicity of nucleotide substitutions.
The vignette also demonstrates how a collection of GWAS hits for asthma can be filtered to SNVs that are "likely pathogenic":
## CHR_ID CHR_POS STRONGEST.SNP.RISK.ALLELE OR.or.BETA MAPPED_TRAIT
## 1 5 14610200 rs16903574-G 1.0862118 asthma
## 2 1 12115601 rs2230624-A 0.1618169 asthma
## 3 9 128721272 rs11539209-A NA asthma
## MAPPED_GENE am_class
## 1 OTULINL likely_pathogenic
## 2 TNFRSF8 likely_pathogenic
## 3 ZDHHC12 likely_pathogenic