REMProduct-class: REMProduct instances

In REMP: Repetitive Element Methylation Prediction

Description

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

Usage

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

showClass("REMProduct")

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