| Title: | Processing of Oxy-Bisulfite Microarray Data |
|---|---|
| Description: | Provides utilities for processing of Oxy-Bisulfite microarray data (e.g. via the Illumina Infinium platform, <http://www.illumina.com>) with tandem arrays, one using conventional bisulfite conversion, the other using oxy-bisulfite conversion. |
| Authors: | E. Andres Houseman, Sc.D. and Kevin C. Johnson |
| Maintainer: | E. Andres Houseman <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.5 |
| Built: | 2025-03-03 04:17:33 UTC |
| Source: | https://github.com/cran/OxyBS |
First derivative of -log(beta pdf) wrt a (first) parameter
diffBeta1(x,a,b)diffBeta1(x,a,b)
x |
beta value |
a |
a parameter (first) |
b |
b parameter (second) |
First derivative of beta minus-log-pdf with respect to first parameter; used for maximum likelihood estimation, not typically called by user.
first derivative with respect to a (first) parameter
E. Andres Houseman
First derivative of -log(beta pdf) wrt b (second) parameter
diffBeta2(x,a,b)diffBeta2(x,a,b)
x |
beta value |
a |
a parameter (first) |
b |
b parameter (second) |
First derivative of beta minus-log-pdf with respect to second parameter; used for maximum likelihood estimation, not typically called by user.
first derivative with respect to b (second) parameter
E. Andres Houseman
Matrix of signal intensitities corresponding to 30 specimens and 30 CpGs.
exampleMethBSexampleMethBS
30 x 30 matrix (CpGs x Specimens)
Matrix of signal intensitities corresponding to 30 specimens and 30 CpGs.
exampleMethOxBSexampleMethOxBS
30 x 30 matrix (CpGs x Specimens)
Matrix of signal intensitities corresponding to 30 specimens and 30 CpGs.
exampleUnmethBSexampleUnmethBS
30 x 30 matrix (CpGs x Specimens)
Matrix of signal intensitities corresponding to 30 specimens and 30 CpGs.
exampleUnmethOxBSexampleUnmethOxBS
30 x 30 matrix (CpGs x Specimens)
Uses maximum likelihood to estimate (C,5mC,5hmC) for one CpG and one specimen
fitOneOxBS(betaBS, betaOxBS, signalBS, signalOxBS, eps=1E-5)fitOneOxBS(betaBS, betaOxBS, signalBS, signalOxBS, eps=1E-5)
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 |
Uses maximum likelihood to estimate (C,5mC,5hmC) for one CpG and one specimen; not typically called by user.
(C,5mC,5hmC) for one CpG and one specimen.
E. Andres Houseman
Uses maximum likelihood to estimate (C,5mC,5hmC) vectors for one specimen
fitOxBS(betaBS, betaOxBS, signalBS, signalOxBS, eps=1E-5)fitOxBS(betaBS, betaOxBS, signalBS, signalOxBS, eps=1E-5)
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 |
Uses maximum likelihood to estimate (C,5mC,5hmC) one specimen (many CpGs).
matrix of (C,5mC,5hmC) values (each row corresponds to a separate CpG).
E. Andres Houseman
## 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)## 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)
Likelihood function for C/5mC/5hmC likelihood estimator
likeOxBS(theta, betaBS, betaOxBS, signalBS, signalOxBS)likeOxBS(theta, betaBS, betaOxBS, signalBS, signalOxBS)
theta |
2-element parameter vector |
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 |
Likelihood function for C/5mC/5hmC likelihood estimator; used for maximum likelihood estimation, not typically called by user.
likelihood for C/5mC/5hmC likelihood
E. Andres Houseman
Score function for C/5mC/5hmC likelihood estimator
scoreOxBS(theta, betaBS, betaOxBS, signalBS, signalOxBS)scoreOxBS(theta, betaBS, betaOxBS, signalBS, signalOxBS)
theta |
2-element parameter vector |
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 |
Score function for C/5mC/5hmC likelihood estimator; used for maximum likelihood estimation, not typically called by user.
score vector for C/5mC/5hmC likelihood
E. Andres Houseman