# Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease 2019)

## Documentation for package ‘CovidMutations’ version 0.1.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

AssayMutRatio | Calculate the mutation detection rate using different assays
assays | Assays for mutation detection using different primers and probes
chinalist | A list of places in China
covid_annot | Mutation annotation results produced by "indelSNP" function
doubleAssay | Detection of co-occurring mutations using double-assay information
gene_position | "GFF3" format gene position data for SARS-Cov-2
gff3 | "GFF3" format annotation data for SARS-Cov-2
globalProteinMut | Global mutational events profiling of proteins
globalSNPprofile | Global single nucleotide polymorphism (SNP) profiling in virus genome
indelSNP | Provide effects of each single nucleotide polymorphism (SNP), insertion and deletion in virus genome
LastfiveNrMutation | Bacth assay analysis for last five Nr of primers
mergeEvents | Merge neighboring events of single nucleotide polymorphism (SNP), insertion and deletion.
MutByGene | Plot mutation counts for certain genes
mutStat | Plot mutation statistics for nucleiotide
nucmer | Mutation information derived from "nucmer" SNP analysis
nucmerr | Preprocessed "nucmer.snps" file using "nucmerRMD" function
nucmerRMD | Preprocess "nucmer" object to add group information
plotMutAnno | Plot the mutation statistics after annotating the "nucmer" object by "indelSNP" function
plotMutProteins | Plot the most frequent mutational events for proteins in the SARS-CoV-2 genome
refseq | SARS-Cov-2 genomic reference sequence from NCBI