RnBiseqSet-class: RnBiseqSet Class

In RnBeads: RnBeads

Description

A class for storing the DNA methylation and quality information from bisulfite sequencing experiments

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

pheno	phenotypic data.
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)
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

Details

TBA

Value

an object of class RnBiseqSet

Slots

status

Normalization status.

Methods and Functions

combine

Combines two datasets.

Author(s)

Pavlo Lutsik

RnBeads documentation built on March 3, 2021, 2 a.m.