AssayMutRatio {CovidMutations}

Calculate the mutation detection rate using different assays

Description

This function is to use the well established assays information to detect mutations in different SARS-CoV-2 genomic sites. The output will be series of figures presenting the mutation profile using a specific assay and a figure for comparison between the mutation detection rate in each primers binding region.

Usage

AssayMutRatio(
  nucmerr = nucmerr,
  assays = assays,
  totalsample = totalsample,
  plotType = "barplot",
  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.

plotType

Figure type for either "barplot" or "logtrans".

outdir

The output directory.

Value

Plot the selected figure type as output.

Examples

data("nucmerr")
data("assays")
Total <- 52 ## Total Cleared GISAID fasta data, sekitseq
#outdir <- tempdir()
#Output the results
AssayMutRatio(nucmerr = nucmerr,
              assays = assays,
              totalsample = Total,
              plotType = "logtrans",
              outdir = NULL)