CovidMutations (version 0.1.3)

LastfiveNrMutation: Bacth assay analysis for last five Nr of primers

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

# NOT RUN {
data("nucmerr")
data("assays")
totalsample <- 434
#outdir <- tempdir()
LastfiveNrMutation(nucmerr = nucmerr,
                   assays = assays,
                   totalsample = totalsample,
                   figurelist = FALSE,
                   outdir = NULL)
# }