BMIQ {RnBeads} | R Documentation

## BMIQ

### Description

This function makes 3 indipendent attempts to fit a 3-state beta mixture model on the provided type I probes. An attempt is successful if at least 4 probes are assigned to each level. In case all attempts fail, the return value is `NULL`.

### Usage

    BMIQ(
      beta.v,
      design.v,
      doH = TRUE,
      nfit = 50000,
      th1.v = c(0.2, 0.75),
      th2.v = NULL,
      niter = 5,
      tol = 0.001
    )

### Arguments

`beta.v` | `double` vector consisting of beta values. Missing values (`NA`s) cannot be handled, so these must be removed or imputed prior to running BMIQ. Before normalization, beta values that are exactly 0 and exactly 1 are replaced by the minimum positive and maximum value below 1, respectively.
`design.v` | `integer` vector of length `length(beta.v)`, containing the values `1` and `2` only. These values specify probe design type.
`doH` | Flag indicating if normalization for hemimethylated type II probes is to be performed.
`nfit` | Number of probes of a given design to use for the fitting. Smaller values will make BMIQ faster at the expense of accuracy. Values between 10000 and 50000 seem to work well.
`th1.v` | Thresholds "type 1" to use for the initialization of the EM algorithm. These values should represent best guesses for calling type I probes hemi-methylated and methylated, and are refined in further steps by the algorithm.
`th2.v` | Thresholds "type 2" to used for the initialization of the EM algorithm. These values should represent best guesses for calling type II probes hemi-methylated and methylated, and are refined in further steps by the EM algorithm. If this is `NULL` (default), the thresholds are estimated based on `th1.v` and a modified PBC correction method.
`niter` | Maximum number of EM iterations to be performed.
`tol` | Tolerance threshold for EM algorithm.

### Details

Performs Beta-mixture quantile normalization, adjusting for type II bias in Infinium 450K data.

### Value

List with the following elements:

`"all"`

  The normalised beta-profile for the sample.

`"class1"`

  Methylation state assigned to the type I probes.

`"class2"`

  Methylation state assigned to the type II probes.

`"av1"`

  Mean beta values for the `nL` classes for type I probes.

`"av2"`

  Mean beta values for the `nL` classes for type II probes.

`"hf"`

  Hubble dilation factor.

`"th1"`

  Estimated thresholds used for type I probes.

`"th2"`

  Estimated thresholds used for type II probes.

### Author(s)

Andrew Teschendorff and Steve Horvath; with minor modifications by Yassen Assenov

[Package RnBeads version 2.12.2 Index]