options: Set or get options for REMP package

In YinanZheng/REMP: Repetitive Element Methylation Prediction

Set or get options for REMP package

Description

Tools to manage global setting options for REMP package.

Usage

remp_options(...)

remp_reset()

Arguments

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

Value

NULL

Supported options

The following options are supported

.default.AluFamily.grep

Regular expression for 'grep' to extract Alu family to be included in the prediction.

.default.L1Family.grep

Regular expression for 'grep' to extract L1 family to be included in the prediction.

.default.ERVFamily.grep

Regular expression for 'grep' to extract ERV family to be included in the prediction.

.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 annotation database (Mar 2020, build hg19).

.default.AH.repeatmasker.hg38

AnnotationHub data ID linked to RepeatMasker annotation database (Sep 2021, build hg38).

.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.

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()

YinanZheng/REMP documentation built on May 14, 2022, 5:58 p.m.