This package provides elementary interfaces to AlphaMissense resources, using BiocFileCache, Rsamtools, and GenomicRanges.
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