tune_parameters {DMRforPairs} | R Documentation

## TUNE MIN_DISTANCE AND MIN_N PARAMETERS

### Description

This function evaluates the number of regions identified for various settings of min_distance and n_min (see `DMRforPairs`). It also summarizes the number of probes available inclusion using a specific setting of recode and the number of probes that is covered by the detected regions.

### Usage

    tune_parameters(parameters,classes_gene,classes_island,targetID, chr, position,m.v,beta.v,recode=1,sep=";",gs,do.parallel=0)

### Arguments

`parameters` | A data frame with two columns: [1] min_distance and [2] min_n. The number of regions / probes will be evaluated for each pair of parameters (per row).
`classes_gene` | Please see `DMRforPairs`
`classes_island` | Please see `DMRforPairs`
`targetID` | Please see `DMRforPairs`
`chr` | Please see `DMRforPairs`
`position` | Please see `DMRforPairs`
`m.v` | Please see `DMRforPairs`
`beta.v` | Please see `DMRforPairs`
`recode` | Please see `DMRforPairs`. (Default=1)
`sep` | Please see `DMRforPairs`. (Default=";")
`gs` | Please see `DMRforPairs`
`do.parallel` | Tuning of the parameters requires a significant amount of compute time and power. Parallelization if offered to do this more efficiently. 0=no parallelization, -1=use all available cores, n>1 use n cores (default=0)

### Details

This function requires a significant amount of compute time/power. Parallelization is highly recommended. When parallelization is enabled, no progress indicator is displayed by R.

### Value

A data frame is returned with the folowing columns

`min_distance` | The setting of min_distance. Also see `DMRforPairs`
`min_n` | The setting for min_n. Also see `DMRforPairs`
`n.regions` | The number of regions identified in your data using the before mentioned combination of settings and the setting of recode.
`n.valid.probes` | The number of probes that were assigned to one or more classes in the `merge_classes` function. This is constant for a specific data set as long as the recode parameter is the same.
`n.probes.included` | The number of probes included in the identified regions.

### Author(s)

Martin Rijlaarsdam

### See Also

`regionfinder`, `DMRforPairs`

### Examples

    data(DMRforPairs_data)
    CL.methy=CL.methy[which(CL.methy$position<=1.07E+8 &
                            CL.methy$position>=1.06E+8),]
    #just two relevant values for the parameters
    #min_distance (100 & 300) and min_n (4 & 8)
    parameters=expand.grid(min_distance = c(200), min_n = c(4,5))
    results_parameters=	tune_parameters(parameters,
    					classes_gene=CL.methy$class.gene.related,
    					classes_island=CL.methy$class.island.related,
    					targetID=CL.methy$targetID,
    					chr=CL.methy$chromosome,
    					position=CL.methy$position,
    					m.v=CL.methy[,c(7:8)],
    					beta.v=CL.methy[,c(11:12)],
    					recode=1,
    					gs=CL.methy$gene.symbol,
    					do.parallel=0)
    results_parameters

[Package DMRforPairs version 1.18.0 Index]