rempTemplate: Prepare data template for REMP

In YinanZheng/REMP: Repetitive Element Methylation Prediction

Prepare data template for REMP

Description

rempTemplate is used to build a set of data templates for prediction. The data templates include RE-CpGs and their methylation data for model training, neighboring CpGs of RE-CpGs and their methylation data for model prediction, and other necessary information about the prediction. This function is useful when one needs to experiment different tunning parameters so that these pre-built data templates can be re-used and substaintially improve efficiency.

Usage

rempTemplate(
  methyDat = NULL,
  Seq.GR = NULL,
  parcel = NULL,
  win = 1000,
  verbose = FALSE
)

Arguments

methyDat	A RatioSet, GenomicRatioSet, DataFrame, data.table, data.frame, or matrix of Illumina BeadChip methylation data (450k or EPIC array) or Illumina methylation percentage estimates by sequencing.
Seq.GR	A GRanges object containing genomic locations of the CpGs profiled by sequencing platforms. This parameter should not be NULL if the input methylation data methyDat are obtained by sequencing. Note that the genomic location can be in either hg19 or hg38 build, but must be consistent with the build as parcel. See details in initREMP.
parcel	An REMParcel object containing necessary data to carry out the prediction. If NULL, the function will search the .rds data file in work.dir exported by initREMP (with export = TRUE) or saveParcel.
win	An integer specifying window size to confine the upstream and downstream flanking region centered on the predicted CpG in RE for prediction. Default = 1000.
verbose	Logical parameter. Should the function be verbose?

Value

A template object containing a GRanges object of neifhboring CpGs of RE-CpGs to be predicted ($NBCpG_GR) and their methylation dataset matrix ($NBCpG_methyDat); a GRanges object of RE-CpGs for model training ($RECpG_GR) and their methylation dataset matrix ($RECpG_methyDat); GRanges objects of RefSeq Gene database ($refgene) and RE ($RE) that are extracted from the parcel input; a string of RE type ($REtype) and a string of methylation platform ($arrayType). Note: the subset operator [] is supported.

Examples

if (!exists("GM12878_450k"))
  GM12878_450k <- getGM12878("450k")
if (!exists("remparcel")) {
  data(Alu.hg19.demo)
  remparcel <- initREMP(arrayType = "450k",
                        REtype = "Alu",
                        annotation.source = "AH",
                        genome = "hg19",
                        RE = Alu.hg19.demo,
                        ncore = 1,
                        verbose = TRUE)
}

template <- rempTemplate(GM12878_450k, 
                         parcel = remparcel, 
                         win = 1000, 
                         verbose = TRUE)
template

## To make a subset
template[1]

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