OxyBS (version 1.0)

fitOxBS: Fit OxyBS for one specimen

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

Value

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

Details

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

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)