Set or get options for REMP package

Description

Tools to manage global setting options for REMP package.

Usage

remp_options(...)

remp_reset()

Arguments

Value

NULL

Supported options

The following options are supported

.default.AluFamily

A list of Alu subfamily to be included in the prediction.

.default.L1Family

A list of L1 subfamily to be included in the prediction.

.default.GM12878.450k.URL

URL to download GM12878 450k methylation profiling data.

.default.AH.repeatmasker.hg19

AnnotationHub data ID linked to RepeatMasker database (build hg19)

.default.AH.refgene.hg19

AnnotationHub data ID linked to refSeq gene database (build hg19)

.default.TSS.upstream

Define the upstream range of transcription start site region.

.default.TSS.downstream

Define the downstream range of transcription start site region.

.default.max.flankWindow

Define the max size of the flanking window surrounding the predicted RE-CpG.

.default.450k.total.probes

Total number of probes designed in Illumina 450k array.

.default.epic.total.probes

Total number of probes designed in Illumina EPIC array.

.default.450k.annotation

A character string associated with the Illumina 450k array annotation dataset.

.default.epic.annotation

A character string associated with the Illumina EPIC array annotation dataset.

.default.genomicRegionColNames

Define the names of the genomic regions for prediction.

.default.predictors

Define the names of predictors for RE methylation prediction.

.default.C.svmLinear.tune

Define the default C (Cost) parameter for Support Vector Machine (SVM) using linear kernel.

.default.sigma.svmRadial.tune

Define the default sigma parameter for SVM using Radial basis function kernel.

.default.C.svmRadial.tune

Define the default C (Cost) parameter for SVM using Radial basis function kernel.

Examples

# Display all default settings
remp_options()

# Display a specified setting
remp_options(".default.max.flankWindow")

# Change default maximum flanking window size to 2000
remp_options(.default.max.flankWindow = 2000)

# Reset all options
remp_reset()