Description Usage Arguments Details Value Author(s) References

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).

1 2 3 4 |

`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 |

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.

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

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

schalkwyk/wateRmelon documentation built on Oct. 27, 2018, 3:26 a.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.