pfilter: Basic data filtering for Illumina 450 methylation data

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

Basic data filtering for Illumina 450 methylation data

Description

The pfilter function filters data sets based on bead count and detection p-values. The user can set their own thresholds or use the default pfilter settings. pfilter will take data matrices of beta values, signal intensities and annotation data, but will also take methylumi (MethyLumiSet) or minfi (RGChannelSetExtended) objects. However it has come to our attention that data read in using the various packages and input methods will give subtly variable data output as they calculate detection p-value and beta values differently, and do/don?t give information about beadcount. The pfilter function does not correct for this, but simply uses the detection p-value and bead count provided by each package.

Usage

pfilter(mn, un, bn, da, pn, bc, perCount=NULL, pnthresh = NULL, perc = NULL, 
pthresh = NULL,logical.return=FALSE)

Arguments

mn	matrix of methylated signal intensities, each column representing a sample (default method), or an object for which a method is available e.g MethyLumiSet or RGChannelSetExtended. N.B. Bead count filtering will not work unless data read in as an RGGhannelSetExtended rather than an RGChannelSet.
un	matrix of unmethylated signal intensities, each column representing a sample (default method) or NULL when mn is a MethyLumiSet or RGChannelSetExtended object
bn	matrix of precalculated betas, each column representing a sample, or NULL when mn is a MethyLumiSet or RGChannelSetExtended object
da	annotation data frame, such as x@featureData@data #methylumi package, or NULL when mn is a MethyLumiSet or RGChannelSetExtended object
pn	matrix of detection p-values, each column representing a sample, a MethyLumiSet or RGChannelSetExtended object
bc	matrix of arbitrary values, each column representing a sample and eeach row representing a probe, in which "NA" represents beadcount <3, or NULL when mn is a MethyLumiSet or RGChannelSetExtended object
perCount	remove sites having this percentage of samples with a beadcount <3, default set to 5
pnthresh	cutoff for detection p-value, default set to 0.05
perc	remove samples having this percentage of sites with a detection p-value greater than pnthresh, default set to 1
pthresh	remove sites having this percentage of samples with a detection p-value greater than pnthresh, default set to 1
logical.return	If it is TRUE, FALSE or TRUE is returned to indicate success

Value

a filtered MethyLumiSet or

a list of the filtered matrices:

mn : methylated intensities

un : unmethylated intensities

bn : betas

da : feature data

or

a filtered MethylSet object.

Methods

signature(mn = "MethyLumiSet")

This is used for performing the pfilter method on MethyLumiSet objects produced by methylumiR.

signature(mn = "RGChannelSetExtended")

This is used for performing the pfilter method on RGChannelSetExtended objects produced by minfi.

Note

Adjusted RGChannelSetExtended methods - 12/10/2015 Now outputs a MethylSet object using preprocessRaw from minfi.

Author(s)

[e-mail]

References

[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)

Examples

# MethyLumiSet method
data(melon)
melon.pf <- pfilter(melon)

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.