fitOxBS: Fit OxyBS for one specimen

In OxyBS: Processing of Oxy-Bisulfite Microarray Data

Description

Uses maximum likelihood to estimate (C,5mC,5hmC) vectors for one specimen

Usage

fitOxBS(betaBS, betaOxBS, signalBS, signalOxBS, eps=1E-5)

Arguments

betaBS	beta value from conventional bisulfite conversion
betaOxBS	beta value from oxy-bisulfite conversion
signalBS	total signal from conventional bisulfite conversion
signalOxBS	total signal from oxy-bisulfite conversion
eps	small positive value representing numerical zero

Details

Uses maximum likelihood to estimate (C,5mC,5hmC) one specimen (many CpGs).

Value

matrix of (C,5mC,5hmC) values (each row corresponds to a separate CpG).

Author(s)

E. Andres Houseman

Examples

## Not run: 
data(OxyBSSampleData)

nSpecimens <- 30
nCpGs <- 30

# Calculate Total Signals
signalBS <- exampleMethBS+exampleUnmethBS
signalOxBS <- exampleMethOxBS+exampleUnmethOxBS

# Calculate Beta Values
betaBS <- exampleMethBS/signalBS
betaOxBS <- exampleMethOxBS/signalOxBS

# Create container for results
MethOxy <- array(NA,dim=c(nCpGs,nSpecimens,3))
dimnames(MethOxy) <- list(
  rownames(exampleMethBS)[1:nCpGs],
  colnames(exampleMethBS)[1:nSpecimens],
  c("C","5mC","5hmC"))

# Process results (one array at a time)
for(i in 1:nSpecimens){
  MethOxy[,i,] <- fitOxBS(betaBS[,i],betaOxBS[,i],signalBS[,i],signalOxBS[,i])
}

# Check that results sum to one
table(apply(MethOxy,1:2,sum))

# First specimen
MethOxy[,1,]

# Ranges
range(MethOxy[,,1])
range(MethOxy[,,2])
range(MethOxy[,,3])

## End(Not run)

OxyBS documentation built on May 2, 2019, 8:51 a.m.