makeMELON: Normalize data from DNA methylation experiments according to...

In MELON: Methylation Enriched LOci Normalization (MELON) for genome-wide DNA methylation experiments

Description

Function to create a normalized MELON object for DNA methylation experimental data

Usage

makeMELON(object, method = c("Max","Clean"), regrwindow = 201, minC = 50, manC = NULL, maxL = 20000, refsample = NULL, doplot = F, savedir = NULL, savefile = NULL, tracefile = NULL)

Arguments

object	raw data, either a dataframe or a matrix
method	indicating the selected criterion to determine the optimal number of used heavily methylated loci. Current implementations foresee Max, corresponding with the highest CME, and Clean, corresponding with the highest increase in consistent methylation enrichment (CME) for increasing L.
regrwindow	local regression window, parameter needed for method Clean. The parameter should be a positive odd integer, default value is 201.
minC	minimum number of stable loci needed in the algorithm. The default is 50.
manC	number of stable loci desired for the algorithm. The default is the number of loci in the full dataset.
maxL	maximal number of considered heavily methylated loci in the algorithm. The default value is 20000.
refsample	index of sample identified as reference sample. If missing, the sample with the largest amount of unique intensities is used as reference.
doplot	logical indicating whether a stability plot should be drawn. This figure plots the consistent methylation enrichment (CME) quantity against the most heavily methylated loci (L) and displays the finally selected L and corresponding CME.
savedir	the directory where to save the plot if doplot == T
savefile	the filename for the plot if doplot == T. If doplot == T, the default name is StabilityPlot (pdf).
tracefile	a writable connection or a character string naming the file to write to, or NULL to stop sink-ing.

Details

A technical description of the algorithm and performance is given in the article 'Methylation Enriched LOci Normalization (MELON) for genome-wide DNA methylation experiments' (De Meyer et al. 2012).

Value

An object of class MELON

Note

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Author(s)

Peter Pipelers <[e-mail]>

References

De Meyer Tim, Pipelers Peter, Szarc vel Szic Katarzyna, Denil Simon, Trooskens Geert, Renard Jean-Pierre, De Keulenaer Sarah, Vanden Berghe Wim and Van Criekinge Wim (2012) Methylation Enriched LOci Normalization (MELON) for genome-wide DNA methylation experiments.

See Also

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Examples

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MELON documentation built on May 2, 2019, 6:21 p.m.