db1 {wateRmelon} | R Documentation

## Internal wateRmelon functions for calculating betas

### Description

db1 is used for quantile normalizing methylated together with unmethylated (dye bias methods nanet, nanes, danes and danet. dfs* functions are used for smoothing the background equalization in methods whose names start with d (daten etc).

### Usage

    db1(mn, un)
    dfsfit(mn, onetwo, roco=substring(colnames(mn), regexpr("R0[1-9]C0[1-9]", colnames(mn))), ... )

    dfs2(x, onetwo)

### Arguments

`mn, x` | matrix of methylated signal intensities, each column representing a sample (default method), or an object for which a method is available. For dfsfit and dfs2 this can also be a matrix of unmethylated intensities.
`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.
`onetwo` | character vector or factor of length nrow(mn) indicating assay type 'I' or 'II'
`roco` | roco for dfsfit giving Sentrix rows and columns. This allows a background gradient model to be fit. This is split from data column names by default. roco=NULL disables model fitting (and speeds up processing), otherwise roco can be supplied as a character vector of strings like 'R01C01' (3rd and 6th characters used).
`...` | no additional arguments currently used

### Details

db1 - quantile normalizes methylated against unmethylated (basic function for dyebuy* dye bias methods). dfsfit - corrects the difference in backgrounds between type I and type II assays and fits a linear model to Sentrix rows and columns if these are available to improve precision where there is a background gradient. dfs2 - finds the difference between type I and type II assay backgrounds for one or more samples.

### Value

db1 - a list of 2 matrices of intensities, methylated and unmethylated dfsfit - a matrix of adjusted intensities dfs2 - a background offset value

### Author(s)

Leonard.Schalkwyk@kcl.ac.uk

### References

Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

[Package wateRmelon version 1.30.0 Index]