UniD.BMIQ: Type II probe normalization-BMIQ

In JieYang031/UniD: Unified Diagnostic Platform for Gliomas

Description

Used to normalize the data generated from 450k or higher platform. Due to the two types of probes used in those platforms, the beta value generated from the Type I and Type II probe is not directly comparable. For the gene expression subtype prediction, data needs to be normalized using BMIQ. Apply.BMIQ was utilised within UniD.BMIQ with all default settings. No need to change.

Usage

UniD.BMIQ(Beta.raw = Beta.raw, arrayType, outDir, write)

Apply.BMIQ(beta.v, design.v, nL = 3, doH = TRUE, nfit = 50000,
  th1.v = c(0.2, 0.75), th2.v = NULL, niter = 5, tol = 0.001,
  plots = FALSE, sampleID = 1)

Arguments

Beta.raw	The raw beta value data frame generated by UniD.dataqc, with missing value.
arrayType	the platform which raw data generated, can be "450k" or "EPIC"
outDir	directory where output data should be saved if write = T
write	whether the output should be saved, highly recommended
beta.v	vector consisting of beta-values for a given sample
design.v	vector specifying the probe Type (I = 1 or II = 2)
nL	number of states in beta mixture model, default is 3
doH	perform normalisation for hemimethylated Type II probes, default is T
nfit	number of probes of a given design to use for fitting, default is 50000
th1.v	thresholds used for the initialisation of the EM-algorithm, default is between 0.2 and 0.75
th2.v	thresholds used for the initialisation of the EM-algorithm, default is NULL
niter	maximum number of EM iterations to do, default is 5
tol	tolerance threshold for EM algorithm, default is 0.001
plots	whether plot the figure, default is FALSE
sampleID	the ID of the sample being normalised, default is 1

Value

A data frame with the normalized data

Functions

• Apply.BMIQ: Apply the BMIQ normalization

References

Teschendorff, A. E., et al. (2013). "A beta-mixture quantile normalization method for correcting probe #' design bias in Illumina Infinium 450 k DNA methylation data." Bioinformatics 29(2): 189-196.

See Also

The BMIQ normalization method is refer to BMIQ

Examples

## Not run: 
Beta.BMIQ <- UniD.BMIQ(Beta.raw, outDir = "~/Desktop/output/",
arrayType = "EPIC", write = T)

Beta.BMIQ <- UniD.BMIQ(Beta.raw,  outDir = NULL,
arrayType = "EPIC", write = F)

## End(Not run)

JieYang031/UniD documentation built on May 5, 2021, 5:16 p.m.