meffil.add.cell.type.reference: Create a cell type reference object
In perishky/meffil: Efficient algorithms for DNA methylation

meffil.add.cell.type.reference

R Documentation

Create a cell type reference object

Description

Create a cell type reference object for estimating cell counts with the Infinium HumanMethylation450 BeadChip.

Usage

meffil.add.cell.type.reference(
  name,
  M,
  U,
  cell.types,
  chip = NA,
  featureset = chip,
  number.sites = 50,
  specific.sites = NULL,
  number.quantiles = 500,
  subsets = NULL,
  object = NULL,
  description = NULL,
  verbose = F
)

Arguments

`name`	Character string providing the name of the reference.
`M`	Matrix of methylated probe intensities (rows=CpG sites, columns=samples).
`U`	Matrix of unmethylatd probe intensities (rows=CpG sites, columns=samples).
`cell.types`	Vector of cell type names corresponding to sample `basename`s.
`chip`	Name returned by `meffil.list.chips()` (Default: NA).
`featureset`	Name returned by `meffil.list.featuresets()` (Default: chip).
`number.sites`	Number of probes to characterise cell type methylation (Default: 50). For each cell type, this number of probes with greater methylation than other cell types and the same number with lesser methylation than the other cell types will be included.
`specific.sites`	If not null (default), then `number.sites` is ignored and the supplied site identifiers are used to differentiate between cell types instead of those maximally different between the cell types within the reference.
`number.quantiles`	Length of numeric sequence to specify probe intensity distributions (Default: 500).
`object`	Cell type reference previously created by this function. If not `NULL`, then this reference is added and all other function arguments are ignored (Default: NULL).
`description`	Text description of the reference (Default: NULL).
`verbose`	If `TRUE`, then status messages are printed during execution (Default: `FALSE`).

Value

A list specifying a cell type reference object that can be used by meffil.estimate.cell.counts() to estimate cell counts in another dataset. The object is a list containing:

beta The normalized methylation values of sites differentially methylated between cell types.
quantiles The average quantiles of methylated and unmethylated signals of probe sets defined by subsets (see below). e.g. quantiles[[name]]$M provides the quantiles (number.quantiles quantiles) of the probes specified by subsets[[name]].
subsets Probes on the microarray partitioned by relationship to CpG islands, either in an island, in a shore or far from an island.