tune_parameters: TUNE MIN_DISTANCE AND MIN_N PARAMETERS

In DMRforPairs: DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

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  

DMRforPairs documentation built on Nov. 8, 2020, 4:52 p.m.