pfilter.gds {bigmelon}R Documentation

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

remove sites having this 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

remove sites having this percentage of sample with a detection p-value greater than pnthresh, default = 1

Value

See pfilter. If using pfilter.gds, function will return a list of two elements. Both logical vectors with length(nrow) and length(ncol), which can be used for subsetting. Otherwise will be used to subset data directly.

Author(s)

Tyler Gorrie-Stone, Original (wateRmelon) Function by Ruth Pidsley

See Also

pfilter

Examples

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

[Package bigmelon version 1.6.0 Index]