REMProduct-class: REMProduct instances

Description Usage Arguments Value Accessors Utilities Examples

Description

Class REMProduct is to maintain RE methylation prediction results. REMProduct inherits Bioconductor's RangedSummarizedExperiment class.

Usage

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REMProduct(
  REtype = "Unknown",
  genome = "Unknown",
  platform = "Unknown",
  win = "Unknown",
  predictModel = "Unknown",
  QCModel = "Unknown",
  rempM = NULL,
  rempB = NULL,
  rempQC = NULL,
  cpgRanges = GRanges(),
  sampleInfo = DataFrame(),
  REannotation = GRanges(),
  RECpG = GRanges(),
  regionCode = DataFrame(),
  refGene = GRanges(),
  varImp = DataFrame(),
  REStats = DataFrame(),
  GeneStats = DataFrame(),
  Seed = NULL
)

rempM(object)

rempB(object)

rempQC(object)

rempAnnot(object)

rempImp(object)

rempStats(object)

remplot(object, ...)

details(object)

decodeAnnot(object, ...)

rempTrim(object, ...)

rempAggregate(object, ...)

rempCombine(object1, object2)

## S4 method for signature 'REMProduct'
rempM(object)

## S4 method for signature 'REMProduct'
rempB(object)

## S4 method for signature 'REMProduct'
rempQC(object)

## S4 method for signature 'REMProduct'
rempImp(object)

## S4 method for signature 'REMProduct'
rempAnnot(object)

## S4 method for signature 'REMProduct'
rempStats(object)

## S4 method for signature 'REMProduct'
remplot(object, type = c("individual", "overall"), ...)

## S4 method for signature 'REMProduct'
details(object)

## S4 method for signature 'REMProduct'
decodeAnnot(object, type = c("symbol", "entrez"), ncore = 1, BPPARAM = NULL)

## S4 method for signature 'REMProduct'
rempTrim(object, threshold = 1.7, missingRate = 0.2)

## S4 method for signature 'REMProduct'
rempAggregate(object, NCpG = 2, ncore = 1, BPPARAM = NULL)

## S4 method for signature 'REMProduct,REMProduct'
rempCombine(object1, object2)

Arguments

REtype

Type of RE ("Alu", "L1", or "LTR").

genome

Specify the build of human genome. Can be either "hg19" or "hg38".

platform

Illumina methylation profiling platform ("450k" or "EPIC").

win

Flanking window size of the predicting RE-CpG.

predictModel

Name of the model used for prediction.

QCModel

Name of the model used for prediction quality evaluation.

rempM

Predicted methylation level in M value.

rempB

Predicted methylation level in beta value (optional).

rempQC

Prediction quality scores, which is available only when Random Forest model is used in remp.

cpgRanges

Genomic ranges of the predicting RE-CpG.

sampleInfo

Sample information.

REannotation

Annotation data for the predicting RE.

RECpG

Annotation data for the RE-CpG profiled by Illumina platform.

regionCode

Internal index code defined in refGene for gene region indicators.

refGene

refSeq gene annotation data, which can be obtained by fetchRefSeqGene.

varImp

Importance of the predictors.

REStats

RE coverage statistics, which is internally generated in remp.

GeneStats

Gene coverage statistics, which is internally generated in remp.

Seed

Random seed for Random Forest model for reproducible prediction results.

object

A REMProduct object.

...

For plot: graphical parameters to be passed to the plot method.

object1

A REMProduct object.

object2

A REMProduct object.

type

For plot and decodeAnnot: see Utilities.

ncore

For decodeAnnot and rempAggregate: number of cores used for parallel computing. By default no parallel computing is allowed (ncore = 1).

BPPARAM

For decodeAnnot and rempAggregate: an optional BiocParallelParam instance determining the parallel back-end to be used during evaluation. If not specified, default back-end in the machine will be used.

threshold

For rempTrim: see Utilities.

missingRate

For rempTrim: see Utilities.

NCpG

For rempAggregate: see Utilities.

Value

An object of class REMProduct for the constructor.

Accessors

rempM(object)

Return M value of the prediction.

rempB(object)

Return beta value of the prediction.

rempQC(object)

Return prediction quality scores.

rempImp(object)

Return relative importance of predictors.

rempStats(object)

Return RE and gene coverage statistics.

rempAnnot(object)

Return annotation data for the predicted RE.

Utilities

remplot(object, type = c("individual", "overall"), ...)

Make a density plot of predicted methylation (beta values) in the REMProduct object. If type = "individual", density curves will be plotted for each of the samples; If type = "overall", one density curve of the mean methylation level across the samples will be plotted. Default type = "individual".

details(object)

Display detailed descriptive statistics of the predicion results.

decodeAnnot(object, type = c("symbol", "entrez")), ncore = NULL, BPPARAM = NULL

Decode the RE annotation data by Gene Symbol (when type = "Symbol") or Entrez Gene (when type = "Entrez").Default type = "Symbol". Annotation data are provided by org.Hs.eg.db.

rempTrim(object, threshold = 1.7, missingRate = 0.2)

Any predicted CpG values with quality score < threshold (default = 1.7, specified by threshold = 1.7) will be replaced with NA. CpGs contain more than missingRate * 100 rate across samples will be discarded. Relavant summary statistics will be re-evaluated.

rempAggregate(object, NCpG = 2, ncore = NULL, BPPARAM = NULL)

Aggregate the predicted RE-CpG methylation by RE using mean. To ensure the reliability of the aggregation, by default only RE with at least 2 predicted CpG sites (specified by NCpG = 2) will be aggregated.

rempCombine(object1, object2)

Combine two REMProduct objects by column.

Examples

1
showClass("REMProduct")

REMP documentation built on Nov. 8, 2020, 8:05 p.m.