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

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Documentation for package ‘CovidMutations’ version 0.1.3

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