SPIAssay (version 1.0.0)

SPIAPlot: Function to visualize the result of the SPIA test

Description

Function SPIAPlot allows the user to rapidly visualize the result of the SPIA test.

Usage

SPIAPlot(SPIAanalysis)

Arguments

SPIAanalysis

The result of the SPIATest function

Value

A plot of the SPIA test

Examples

# An example of genotype calls with:
# - four cell lines
# - for each cell line five SNP calls
GenotypeCalls <- rbind(
c("SNP1", "AA", "AA", "AB", "AB"),
c("SNP2", "NoCall", "AA", "AB", "AB"),
c("SNP3", "AB", "AB", "AA" , "AB"),
c("SNP4", "BB", "BB", "BB", "BB"),
c("SNP5", "AB", "BB", "AA", "AA"))
colnames(GenotypeCalls) <- c("SNP_ID","CellLine1","CellLine2","CellLine3","CellLine4")

# Encode the data into SPIA format.
# SPIA uses 0 for AA, 1 for BB, 2 for AB, and NA for NoCall
# therefore, GenotypeCalls has to be encoded by meand of
# toSPIAData
encoding <- c("AA","BB","AB","NoCall")
SPIAGenotypeCalls <- toSPIAData(GenotypeCalls,encoding)


# Perform SPIA analysis
SPIAParam <- list(Pmm = 0.1, nsigma = 1, Pmm_nonM = 0.6, nsigma_nonM = 1, PercValidCall=0.7)
SPIAanalysis <- SPIATest(SPIAGenotypeCalls, row.names = TRUE, test.prob = TRUE, SPIAParam)

# Plot summary
SPIAPlot(SPIAanalysis)