options: Set or get options for REMP package
In REMP: Repetitive Element Methylation Prediction

Description Usage Arguments Value Supported options Examples

Tools to manage global setting options for REMP package.

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remp_options(...)

remp_reset()

...

Option names to retrieve option values or [key]=[value] pairs to set options.

NULL

The following options are supported

.default.AluFamily.grep: Regular expression for 'grep' to extract Alu subfamily to be included in the prediction.
.default.L1Family.grep: Regular expression for 'grep' to extract L1 subfamily to be included in the prediction.
.default.LTRFamily.grep: Regular expression for 'grep' to extract Long Terminal Repeat (LTR), including Endogenous Retrovirus (ERV) subfamily to be included in the prediction (this includes Human Endogenous Retrovirus, HERV).
.default.chr: List of human chromosome.
.default.GM12878.450k.URL: URL to download GM12878 450k methylation profiling data.
.default.RMSK.hg19.URL: URL to download RepeatMasker database in hg19 genome.
.default.RMSK.hg38.URL: URL to download RepeatMasker database in hg38 genome.
.default.refGene.hg19.URL: URL to download refSeq gene database in hg19 genome.
.default.refGene.hg38.URL: URL to download refSeq gene database in hg38 genome.
.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.AH.hg38ToHg19.over.chain: AnnotationHub hg38 to hg19 liftover chain data ID.
.default.AH.hg19ToHg38.over.chain: AnnotationHub hg19 to hg38 liftover chain data ID.
.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.27k.total.probes: Total number of probes designed in Illumina 27k array.
.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.svmLinear.tune: Define the default C (Cost) parameter for Support Vector Machine (SVM) using linear kernel.
.default.svmRadial.tune: Define the default parameters (C and sigma) for SVM using Radial basis function kernel.
.default.xgbTree.tune: Define the default parameters (nrounds, eta, max_depth, gamma, colsample_bytree, min_child_weight, and subsample) for Extreme Gradient Boosting.

# 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()