doubleAssay {CovidMutations}

Detection of co-occurring mutations using double-assay information

Description

The detection of SARS-CoV-2 is important for the prevention of the outbreak and management of patients. Real-time reverse-transcription polymerase chain reaction (RT-PCR) assay is one of the most effective molecular diagnosis strategies to detect virus in clinical laboratory. It will be more accurate and practical to use double assays to detect some samples with co-occurring mutations.

Usage

doubleAssay(nucmerr = nucmerr, assay1 = assay1, assay2 = assay2, outdir = NULL)

Arguments

nucmerr

Mutation information containing group list(derived from "nucmer" object using "nucmerRMD" function).

assay1

Information of the first assay(containing primers locations and probe location, see the format of assays provided as example data. e.g. data(assays); assay1<- assays[1,])

assay2

Information of the second assay, the format is the same as the first assay.

outdir

The output directory. If NULL print the plot in Rstudio.

Value

Plot three figures in a single panel, including two results of assays and a "venn" plot for co-occurring mutated samples.

Examples

data("nucmerr")
data("assays")
assay1 <- assays[1,]
assay2 <- assays[2,]
#outdir <- tempdir()
doubleAssay(nucmerr = nucmerr,
            assay1 = assay1,
            assay2 = assay2,
            outdir = NULL)