OxyBS: Processing of Oxy-Bisulfite Microarray Data

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Provides utilities for processing of Oxy-Bisulfite microarray data (e.g. via the Illumina Infinium platform) with tandem arrays, one using conventional bisulfite sequencing, the other using oxy-bisulfite sequencing.

Author
E. Andres Houseman, Sc.D. and Kevin C. Johnson
Date of publication
2015-12-01 16:17:17
Maintainer
E. Andres Houseman <andres.houseman@oregonstate.edu>
License
GPL (>= 2)
Version
1.0

View on CRAN

Man pages

diffBeta1
First derivative of beta minus-log-pdf with respect to first...
diffBeta2
First derivative of beta minus-log-pdf with respect to second...
exampleMethBS
Sample Data: Methylation (red) signals from conventional...
exampleMethOxBS
Sample Data: Methylation (red) signals from oxy-bisulfite...
exampleUnmethBS
Sample Data: Unmethylated (green) signals from conventional...
exampleUnmethOxBS
Sample Data: Unmethylated (green) signals from oxy-bisulfite...
fitOneOxBS
Fit one OxyBS result
fitOxBS
Fit OxyBS for one specimen
likeOxBS
Likelihood function for C/5mC/5hmC likelihood estimator
rfEwasExampleCovariate
Simulated covariate for mixed-cell DNA methylation data set
scoreOxBS
Score function for C/5mC/5hmC likelihood estimator

Files in this package

OxyBS
OxyBS/NAMESPACE
OxyBS/data
OxyBS/data/OxyBSSampleData.RData
OxyBS/R
OxyBS/R/OxyBS.R
OxyBS/MD5
OxyBS/DESCRIPTION
OxyBS/man
OxyBS/man/fitOxBS.Rd
OxyBS/man/exampleUnmethBS.Rd
OxyBS/man/exampleMethOxBS.Rd
OxyBS/man/exampleMethBS.Rd
OxyBS/man/diffBeta2.Rd
OxyBS/man/scoreOxBS.Rd
OxyBS/man/likeOxBS.Rd
OxyBS/man/fitOneOxBS.Rd
OxyBS/man/exampleUnmethOxBS.Rd
OxyBS/man/diffBeta1.Rd
OxyBS/man/rfEwasExampleCovariate.Rd