Bigmelon Quantile Normalization methods.

Description

Functions used to perform quantile normalization on gds.class objects

Usage

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## 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)
design.qn.gdsn(gds, target, newnode, onetwo)
db.gdsn(gds, mns, uns)
dfsfit.gdsn(gds, targetnode, newnode, roco, onetwo)

Arguments

gds

A gds.class object

node

"name" of desired output gdsn.class node

mns

gdsn.class node that corresponds to "methylated" intensities.

uns

gdsn.class node that corresponds to "unmethylated" intensities.

onetwo

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

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 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 ("temp.gds") in the current working directory and is remove it when normalization is complete. Current methods supplied by default arguments will replace the raw intensities with normalized intensities.

Value

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

Author(s)

Tyler J Gorrie-Stone <tgorri@essex.ac.uk>

See Also

wateRmelon, dasen

Examples

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