remprofile: Extract DNA methylation data profiled in RE
In REMP: Repetitive Element Methylation Prediction

Description Usage Arguments Value Examples

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

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
)

`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?

A REMProduct object containing profiled RE methylation results.

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)