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]