CNV.load: CNV.load

In conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Description

Prepare combined intensities from various input objects.

Usage

CNV.load(input, ...)

## S4 method for signature 'GenomicRatioSet'
CNV.load(input, names = NULL)

## S4 method for signature 'MethylSet'
CNV.load(input, names = NULL)

## S4 method for signature 'data.frame'
CNV.load(input, names = NULL)

## S4 method for signature 'matrix'
CNV.load(input, names = NULL)

## S4 method for signature 'numeric'
CNV.load(input, names = NULL)

Arguments

input	Object of MethylSet class (minfi package), data.frame class, matrix class or numeric class.
...	Additional parameters (CNV.load generic, currently not used).
names	Vector specifying sample names. If not supplied, colnames are used. For MethylSet input, the first column of pData(input) matching 'name' (grep) is used.

Details

This method gathers combined intensities of the Methylated and Unmethylated signals for all supplied probes. Probe IDs must be supplied as row names or in a seperate column named 'ID_REF' or 'TargetID'. If column names match 'intensity', only those columns are used. Else, if column names match 'signal' or 'methylated', only those columns are used. Otherwise, all columns are used.

Value

CNV.data object.

Author(s)

Volker Hovestadt [e-mail]

Examples

library(minfiData)
d <- CNV.load(MsetEx)
d

conumee documentation built on Nov. 8, 2020, 6 p.m.