SPIAssay (version 1.1.0)

SPIATest: Function to compute SPIA test

Description

Function SPIATest computes SPIA distance and performs probabilistic test on a set of cell lines.

Usage

SPIATest(x, row.names = TRUE, test.prob = TRUE, test.param = list(Pmm=0.1, nsigma=2,  Pmm_nonM=0.6, nsigma_nonM=3,  PercValidCall=0.9), verbose = FALSE)

Arguments

x

a matrix with a column for each cell line and a row for each SNP

row.names

specify if the first column of x contains SNPs names/identificators

test.prob

specify if the function has to perform SPIA probabilistic test

test.param

specify the parameters of the probabilistic test.

• Pmm: SNP probability of mismatch in a matching population
• nsigma: area limit for Pmm
  • Pmm_nonM: SNP probability of mismach in a non matching population
  • nsigma_nonM: area limit for Pmm_nonM
  • PercValidCall: percentage of valid SNP calls to consider the test valid

verbose

print verbose information

Value

Examples

library(SPIAssay)

# 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
SPIAanalysis <- SPIATest(SPIAGenotypeCalls)
# This analysis give an error because there are not enough SNPs

# Perform SPIA analysis with parameters SPIAParam 
# to reduce the 'similar' region
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)