Usage
RnBiseqSet(pheno, sites, meth, covg = NULL, assembly = "hg19", target = "CpG", summarize.regions = TRUE, region.types = rnb.region.types.for.analysis(assembly), useff = rnb.getOption("disk.dump.big.matrices"), usebigff = rnb.getOption("disk.dump.bigff"), verbose = FALSE)
Arguments
sites
CpG site definition, as a data.frame
with 3 variables: chromosome (of type
character), position (integer) and
strand (character, one of "+", "-" or "*"
meth
summarized methylation calls as a matrix or ff_matrix
covg
read coverage information as a matrix or ff_matrix
assembly
the genome assembly
target
target DNA methylation features (CpG sites)
region.types
region annotations for which the methylation data should be summarized
useff
flag specifying whether the ff functionality should be used
usebigff
flag specifying whether the extended ff functionality should be used (large matrix support for ff)
verbose
flag specifying whether the diagnostic messages should be written to the
console or to the RnBeads logger, if the latter is initialized