MutByGene: Plot mutation counts for certain genes

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

Description

After annotating the mutations, this function is to plot the counts of mutational events for each gene in the SARS-CoV-2 genome.

Usage

MutByGene(nucmerr = nucmerr, gff3 = gff3, figurelist = FALSE, outdir = NULL)

Arguments

nucmerr	Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).
gff3	"GFF3" format gene position data for SARS-Cov-2(the "GFF3" file should include columns named: "Gene", "Start", "Stop").
figurelist	Whether to output the integrated plot list for each gene.
outdir	The output directory, if the figurelist = TRUE, output the figure in the R session.

Value

Plot the mutation counts figure for each gene as output.

Examples

data("nucmerr")
data("gene_position")
#outdir <- tempdir()
MutByGene(nucmerr = nucmerr, gff3 = gene_position, figurelist = FALSE, outdir = NULL)
#if figurelist = TRUE, the recommendation for figure display(in pixel)is: width=1650, height=1300

CovidMutations documentation built on Sept. 18, 2020, 5:06 p.m.