Amino Acid Annotation (A3) Format

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Documentation for package ‘rtemis.a3’ version 0.5.3

• DESCRIPTION file
• Package README

Help Pages

rtemis.a3-package	rtemis.a3: Amino Acid Annotation format
aa_sub	Perform amino acid substitutions
annotation_position	Create position-based annotations for A3
annotation_range	Create range-based annotations for A3
annotation_variant	Create variant annotations for A3
clinvar_variants	Fetch ClinVar variants for a gene and parse them into A3Variant objects
concat	Concatenate character vector to single string for sequence input
create_A3	Create an A3 object from sequence, annotations, and metadata
gene2sequence	Get the coding sequence of a gene
get_alphafold	Get AlphaFold info for a given UniProt ID
pdb_annotations	Fetch PDB structural annotations for a UniProt accession
read_A3json	Read 'A3' object from JSON file
rtemis.a3	rtemis.a3: Amino Acid Annotation format
uniprot_sequence	Fetch a protein sequence from UniProt
uniprot_to_A3	Fetch a UniProt entry and parse it into an A3 object
write_A3json	Write 'A3' object to JSON file