remprofile: Extract DNA methylation data profiled in RE

In REMP: Repetitive Element Methylation Prediction

Description

remprofile is used to extract profiled methylation of CpG sites in RE.

Usage

remprofile(
  methyDat,
  REtype = c("Alu", "L1", "LTR"),
  annotation.source = c("AH", "UCSC"),
  genome = c("hg19", "hg38"),
  Seq.GR = NULL,
  RE = NULL,
  impute = FALSE,
  imputebyrow = TRUE,
  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.
REtype	Type of RE. Currently "Alu", "L1", and "LTR" are supported.
annotation.source	Character parameter. Specify the source of annotation databases, including the RefSeq Gene annotation database and RepeatMasker annotation database. If "AH", the database will be obtained from the AnnotationHub package. If "UCSC", the database will be downloaded from the UCSC website http://hgdownload.cse.ucsc.edu/goldenpath. The corresponding build ("hg19" or "hg38") will be specified in the parameter genome.
genome	Character parameter. Specify the build of human genome. Can be either "hg19" or "hg38". For 450k/EPIC array, "hg19" is used more often while specifying "hg38" will lift over the Illumina CpG probe location to build "hg38". For sequencing data, please make sure the specified genome build is consistent with the actual genome build of Seq.GR.
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. The user should make sure the parameter genome is correctly specified.
RE	A GRanges object containing user-specified RE genomic location information. If NULL, the function will retrive RepeatMasker RE database from AnnotationHub (build hg19) or download the database from UCSC website (build hg19/hg38).
impute	Parameter used by grooMethy. If TRUE, K-Nearest Neighbouring imputation will be applied to fill the missing values. Default = FALSE.
imputebyrow	Parameter used by grooMethy. If TRUE, missing values will be imputed using similar values in row (i.e., across samples); if FALSE, missing values will be imputed using similar values in column (i.e., across CpGs). Default is TRUE.
verbose	Logical parameter. Should the function be verbose?

Value

A REMProduct object containing profiled RE methylation results.

Examples

data(Alu.hg19.demo)
if (!exists("GM12878_450k")) GM12878_450k <- getGM12878("450k")
remprofile.res <- remprofile(GM12878_450k,
                             REtype = "Alu",
                             annotation.source = "AH",
                             genome = "hg19",
                             RE = Alu.hg19.demo,
                             verbose = TRUE)
details(remprofile.res)
rempB(remprofile.res) # Methylation data (beta value)

remprofile.res <- rempAggregate(remprofile.res)
details(remprofile.res)
rempB(remprofile.res) # Methylation data (beta value)

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