LastfiveNrMutation: Bacth assay analysis for last five Nr of primers

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

Description

Last five nucleotides of primer mutation count/type for any reverse transcription polymerase chain reaction (RT-PCR) primer.

Usage

LastfiveNrMutation(
  nucmerr = nucmerr,
  assays = assays,
  totalsample = totalsample,
  figurelist = FALSE,
  outdir = NULL
)

Arguments

nucmerr	Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).
assays	Assays dataframe including the detection ranges of mutations.
totalsample	Total sample number, total cleared GISAID fasta data.
figurelist	Whether to output the integrated plot list for each assay.
outdir	The output directory. if the figurelist = TRUE, output the figure in the R session.

Value

Plot the mutation counts(last five nucleotides for each primer) for each assay as output.

Examples

data("nucmerr")
data("assays")
totalsample <- 434
#outdir <- tempdir()
LastfiveNrMutation(nucmerr = nucmerr,
                   assays = assays,
                   totalsample = totalsample,
                   figurelist = FALSE,
                   outdir = NULL)

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