pfiltergds: Basic data filtering for Illumina methylation data in gds...

In TJGorrie/bigmelon: Illumina methylation array analysis for large experiments

Basic data filtering for Illumina methylation data in gds objects

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. This specific function will take a Genomic Data Structure (GDS) file as input and perform pfilter similar to how pfilter in wateRmelon is performed.

Usage

## S4 method for signature 'gds.class'
pfilter(mn, perCount = NULL, pnthresh = NULL,
perc = NULL, pthresh = NULL)

Arguments

mn	a gds object OR node corresponding to methylated intensities
perCount	Threshold specifying which sites should be removed if they have a given percentage of samples with a beadcount <3, default = 5
pnthresh	cut off for detection p-value, default= 0.05
perc	remove sample having this percentage of sites with a detection p-value greater than pnthresh, default = 1
pthresh	Threshold specifying which sites should be removed if they have a given percentage of samples with a detection p-value greater than pnthresh, default = 1

Value

See pfilter. If using pfilter.gds, function If using pfilter.gds function will return a list of containing two locical vectors of length(nrow) and lneght(ncol) which can be used to subset data. Otherwise if called using pfilter data will be subsetted automatically.

Author(s)

Tyler Gorrie-Stone, Original (wateRmelon) Function by Ruth Pidsley Who to Contact: <[e-mail]

See Also

pfilter

Examples

data(melon)
e <- es2gds(melon, "melon.gds")
pfilter(e)
closefn.gds(e)
unlink("melon.gds")

TJGorrie/bigmelon documentation built on June 12, 2024, 6:19 p.m.