db1: 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=unlist(data.frame(strsplit(colnames(mn), "_"),
                 stringsAsFactors = FALSE)[2, ]), ... )

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.

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

Value

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

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.

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)