Maximum Likelihood Estimation of DNA Methylation and
Hydroxymethylation Proportions
Maximum likelihood estimates (MLE) of the proportions
of 5-mC and 5-hmC in the DNA using information from BS-conversion,
TAB-conversion, and oxBS-conversion methods. One can use information from all three methods
or any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and
Kiihl et al. (2018, to appear).
minfi, microbenchmark, GEOquery, knitr, BiocStyle, rmarkdown

minfi, microbenchmark, GEOquery, knitr, BiocStyle, rmarkdown,
wateRmelon, IlluminaHumanMethylation450kmanifest

minfi, microbenchmark, GEOquery, knitr, BiocStyle, rmarkdown,
IlluminaHumanMethylation450kmanifest

Maximum likelihood estimates (MLE) of the proportions
of 5-mC and 5-hmC in the DNA using information from BS-conversion,
TAB-conversion, and oxBS-conversion methods. One can use information from all three methods
or any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and
Kiihl et al. (2019) <doi:10.1515/sagmb-2018-0031>.

minfi, microbenchmark, GEOquery, knitr, rmarkdown,
IlluminaHumanMethylation450kmanifest

Estimating Frequencies, Prevalence and Multiplicity of Infection
c(person("Meraj", "Hashemi", role = c("cre", "aut", "com"), email = "mhashemi@hs-mittweida.de"),
person("Kristan", "Schneider", role = c("aut", "ths"), email = "kristan.schneider@hs-mittweida.de"))
The implemented methods reach out to scientists that seek to estimate multiplicity of infection (MOI) and lineage (allele) frequencies and prevalences at molecular markers using the maximum-likelihood method described in Schneider (2018) <doi:10.1371/journal.pone.0194148>, and Schneider and Escalante (2014) <doi:10.1371/journal.pone.0097899>. Users can import data from Excel files in various formats, and perform maximum-likelihood estimation on the imported data by the package's moimle() function.
Meraj Hashemi [cre, aut, com],
Kristan Schneider [aut, ths]