CovidMutations (version 0.1.3)

plotMutProteins: Plot the most frequent mutational events for proteins in the SARS-CoV-2 genome

Description

Plot the most frequent mutational events for proteins selected. The protein name should be specified correctly (only for SARS-CoV-2).

Usage

plotMutProteins(
  covid_annot = covid_annot,
  proteinName = "NSP2",
  top = 20,
  outdir = NULL
)

Arguments

covid_annot

The mutation effects provided by "indelSNP" function.

proteinName

Proteins in the SARS-CoV-2 genome, available choices: 5'UTR, NSP1~NSP10, NSP12a, NSP12b, NSP13, NSP14, NSP15, NSP16, S, ORF3a, E, M, ORF6, ORF7a, ORF7b, ORF8, N, ORF10.

top

The number of objects to display.

outdir

The output directory.

Value

Plot the mutational events for selected proteins as output.

Examples

# NOT RUN {
data("covid_annot")
# make sure the covid_annot is a dataframe
covid_annot <- as.data.frame(covid_annot)
#outdir <- tempdir() specify your output directory
plotMutProteins(covid_annot = covid_annot,proteinName = "NSP2", top = 20, outdir = NULL)
# }