RnBiseqSet-class {RnBeads} | R Documentation |
A class for storing the DNA methylation and quality information from bisulfite sequencing experiments
Wrapper function RnBiseqSet
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)
pheno |
phenotypic data. |
sites |
CpG site definition, as a |
meth |
summarized methylation calls as a |
covg |
read coverage information as a |
assembly |
the genome assembly |
target |
target DNA methylation features (CpG sites) |
summarize.regions |
... |
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 |
TBA
an object of class RnBiseqSet
status
Normalization status.
combine
Combines two datasets.
Pavlo Lutsik