as.methylumi-methods: Methods for Function 'as.methylumi'

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

Methods for Function as.methylumi

Description

Returns a MethyLumiSet object populaed with the data provided. There are MethyLumiSet and MethylSet methods. In the default method, the data is all optional. Please note that for the results to be sane, mn, un, bn, and pv have to be in the same sample and feature order and the same size. The function does not currently do any checks!

Usage

# default method
as.methylumi (mn = NULL, un = NULL, bn = NULL, pv = NULL, qc = NULL, da = NULL,...)

Arguments

mn	matrix of methylated signal intensities, each column representing a sample (generic) or a MethyLumiSet, RGSet, or MethylSet object. Column names are used to get Sentrix row and column by default, see '...'.
un	matrix of unmethylated signal intensities, each column representing a sample (default method) or NULL when mn is an object containing methylated and unmethylated values
bn	matrix of precalculated betas, each column representing a sample
pv	matrix of detection p-values, each column representing a sample
da	annotation data frame, such as x@featureData@data #methylumi package. If NULL (the default), the IlluminaHumanMethylation450kmanifest package is used. See the fd argument
qc	control probe intensities: list of 2 matrices, Cy3 and Cy5, with rownames, such as produced by intensitiesByChannel(QCdata(x)) (methylumi package)
...	Other arguments such as a featureData object or optional assayData

Methods

signature(mn = "MethylSet")

Coerces a MethylSet to a MethyLumiSet, and provides it with a set of featureData, which by default is just the chromosome and DESIGN (ie typeI or type II assay). Other data can be included using the fd argument, available data is listed by the function getColumns()

signature(mn = "MethyLumiSet")

This is mainly useful for adding featureData as described under MethylSet above. MethyLumiSet objects produced by methylumiR have the full annotation, those from methylumIDAT do not, and functions such as swan require it

signature(mn = "ANY")

as.methylumi (mn = NULL, un = NULL, bn = NULL, pv = NULL, qc = NULL, da = NULL, fd = c("CHR", "DESIGN"))

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.