run methylCC deconvolution
Usage
run_methylcc(
methyl_set,
array = c("450k", "EPIC"),
find_dmrs_object = NULL,
verbose = TRUE,
epsilon = 0.01,
max_iter = 100,
take_intersection = FALSE,
include_cpgs = FALSE,
include_dmrs = TRUE,
init_param_method = "random",
a0init = NULL,
a1init = NULL,
sig0init = NULL,
sig1init = NULL,
tauinit = NULL,
demo = FALSE,
seed = 1
)Arguments
- methyl_set
A minfi MethylSet
- array
type of methylation array that was used. possible options are '450k' and 'EPIC'
- find_dmrs_object
If the user would like to supply different differentially methylated regions, they can use the output from the find_dmrs function to supply different regions to estimatecc.
- verbose
TRUE/FALSE argument specifying if verbose messages should be returned or not. Default is TRUE.
- epsilon
Threshold for EM algorithm to check for convergence. Default is 0.01.
- max_iter
Maximum number of iterations for EM algorithm. Default is 100 iterations.
- take_intersection
TRUE/FALSE asking if only the CpGs included in object should be used to find DMRs. Default is FALSE.
- include_cpgs
TRUE/FALSE. Should individual CpGs be returned. Default is FALSE.
- include_dmrs
TRUE/FALSE. Should differentially methylated regions be returned. Default is TRUE.
- init_param_method
method to initialize parameter estimates. Choose between "random" (randomly sample) or "known_regions" (uses unmethyalted and methylated regions that were identified based on Reinus et al. (2012) cell sorted data.). Defaults to "random".
- a0init
Default NULL. Initial mean methylation level in unmethylated regions
- a1init
Default NULL. Initial mean methylation level in methylated regions
- sig0init
Default NULL. Initial var methylation level in unmethylated regions
- sig1init
Default NULL. Initial var methylation level in methylated regions
- tauinit
Default NULL. Initial var for measurement error
- demo
TRUE/FALSE. Should the function be used in demo mode to shorten examples in package. Defaults to FALSE.
- seed
fixed seed to account for RNG influences