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wateRmelon (version 1.16.0)

Illumina 450 methylation array normalization and metrics

Description

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

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Version

Version

1.16.0

License

GPL-3

Maintainer

Leo

Last Published

February 15th, 2017

Functions in wateRmelon (1.16.0)

wm_internal

Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
colnames-methods

Methods for Function colnames in Package wateRmelon
betaqn-exprmethy450-methods

Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays
genki

SNP derived performance metrics for Illumina 450K DNA methylation arrays.
beadc

Calculates the number of samples with bead count <3 for each probe in matrix of bead count values
dasen-minfi-methods

Calculate normalized betas from Illumina 450K methylation arrays
outlyx

Identify Outliers within Methylumi and Minfi packaged objects
agep

Age Prediction from methylomic expression data
metrics

Calculate a full set of 450K normalization/performance metrics
pwod-methods

Methods for Function pwod in Package wateRmelon
iDMR

Imprinting differentially methylated region probes of Illumina 450 arrays
beadcount

Creates matrix of beacounts from minfi data.
BMIQ

Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
dasen-methods

Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
bscon

Calculate bisulphite conversion
seabi

Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays
pwod

Probe-Wise Outlier Detection
outlyx-methods

Methods for Function outlyx in Package wateRmelon
got

Internal functions for Illumina i450 normalization functions
dasen

Calculate normalized betas from Illumina 450K methylation arrays
genki-methods

Methods for Function genki in Package wateRmelon
readEPIC

readEPIC
seabi-methods

Methods for Function seabi in Package wateRmelon
genkme

Internal functions for genotype-based normalization metrics
Beta2M

Internal functions for peak.correction (fuks)
combo

Combine MethyLumiSet objects
dmrse-methods

Methods for Function dmrse in Package wateRmelon
sextest

Test Illumina methylation 450K array probes for sex difference (internal function for calculating seabi performance metric)
pfilter

Basic data filtering for Illumina 450 methylation data
as.methylumi-methods

Methods for Function as.methylumi
wateRmelon-package

Illumina 450K arrays: normalization and performance metrics
dmrse

Standard error of iDMR 450k array DNA methylation features
db1

Internal wateRmelon functions for calculating betas
seabird

Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric)
adaptRefQuantiles

Functions from 450-pipeline (Touleimat & Tost)
melon

Small MethyLumi data set for examples and testing
qual

A measure of Normalization Violence