bigmelon-normalization {bigmelon} | R Documentation

## Bigmelon Quantile Normalization methods.

### Description

Set of functions that are used to perform quantile normalization methods on gds.class objects.

### Usage

    ## S4 method for signature 'gds.class'
    dasen(mns, fudge = 100, ret2 = FALSE, node="betas",...)
    dasen.gds(gds, node, mns, uns, onetwo, roco, fudge, ret2)
    qn.gdsn(gds, target, newnode)
    db.gdsn(gds, mns, uns)
    dfsfit.gdsn(gds, targetnode, newnode, roco, onetwo)

### Arguments

`gds` | A gds.class object
`node` | The "name" of desired output `gdsn.class` node
`mns` | The `gdsn.class` node that corresponds to "methylated" intensities.
`uns` | The `gdsn.class` node that corresponds to "unmethylated" intensities.
`onetwo` | The `gdsn.class` node that corresponds to probe designs (in reference to 450k and EPIC arrays) OR character string pointing to location of `gdsn.class` node. e.g. "fData/DESIGN" OR vector containing probe design types of length > 1.
`roco` | 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' (only 3rd and 6th characters used).
`fudge` | The value added to total intensity to prevent denominactors close to zero when calculation betas. default = 100
`ret2` | if TRUE, appends the newly calculated methylated and unmethylated intensities to original gds (as specified in gds arguement). Will overwrite the raw intensities.
`target` | Target `gdsn.class` node to perform normalization on. If using "*****.gds" method you do not need to specify this.
`targetnode` | Target `gdsn.class` node to perform normalization on. If using "*****.gds" method you do not need to specify this.
`newnode` | "name" of desired output `gdsn.class` node. If using "*****.gds" method you do not need to specify this.
`...` | Additional args such as roco or onetwo.

### Details

Each function performs a normalization method described within the wateRmelon package. Functions: `qn.gdsn`, `design.qn.gdsn`, `db.gdsn` and `dfsfit.gdsn` are described to allow users to create their own custom normalization methods. Otherwise calling `dasen` or `dasen.gds` e.t.c will perform the necessary operations for quantile normalization.

Each 'named' normalization method will write a temporary gds object called "temp.gds" into the current working directory and it is removed when normalization is complete. Current methods supplied by default arguments will replace the raw betas with normalized betas, but leave the methylated and unmethylated intensities unprocessed.

### Value

Normalization methods return nothing but will affect the gds file and replace/add nodes given to the function.

### Author(s)

Tyler J Gorrie-Stone <t.gorrie-stone@qmul.ac.uk>

### See Also

`wateRmelon`, `dasen`

### Examples

    data(melon)
    e <- es2gds(melon,'wat_melon.gds')
    dasen(e)
    closefn.gds(e) # Close gds object
    unlink('wat_melon.gds') # Delete Temp file

[Package bigmelon version 1.18.0 Index]