remprofile {REMP}R Documentation

Extract DNA methylation data profiled in RE

Description

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

Usage

remprofile(methyDat, REtype = c("Alu", "L1"), RE = NULL,
  impute = TRUE, 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).

REtype

Type of RE. Currently "Alu" and "L1" are supported.

RE

A GRanges object containing user-specified RE genomic location information. If NULL, the function will retrive RepeatMasker RE database from AnnotationHub (build hg19).

impute

Parameter used by grooMethy. If TRUE, K-Nearest Neighbouring imputation will be applied to fill the missing values. Default = TRUE.

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.demo)
GM12878_450k <- getGM12878('450k')
remp.res <- remprofile(GM12878_450k, REtype = "Alu", RE = Alu.demo)
details(remp.res)
rempB(remp.res) # Methylation data (beta value)

remp.res <- rempAggregate(remp.res)
details(remp.res)
rempB(remp.res) # Methylation data (beta value)
[Package REMP version 1.6.1 Index]