sesamize: "fix" a SummarizedExperiment (for which IDATs may be...

In ttriche/sesamizeGEO: the poor man's methylation suite (cf. `sesamizer`)

"fix" a SummarizedExperiment (for which IDATs may be unavailable) with Sesame

Description

"fix" a SummarizedExperiment (for which IDATs may be unavailable) with Sesame

Usage

sesamize(
  x,
  genome = "hg19",
  BPPARAM = SerialParam(),
  mft = NULL,
  sce = TRUE,
  verbose = FALSE,
  ...
)

Arguments

x	SummarizedExperiment-derived object with assays Red & Green
genome	Which genome should the probes be mapped to? (hg19)
BPPARAM	a BiocParallelParam object (SerialParam())
mft	a data.frame with columns Probe_ID, M, U, and col (guess)
sce	return SingleCellExperiment rather than a RatioSet? (TRUE)
verbose	be verbose? (FALSE)
...	additional arguments passed to openSesame

Value

a sesamized SingleCellExperiment or GenomicRatioSet from x

Examples

  # reprocess some 450k data from an existing RGChannelSet 
  if (require(FlowSorted.CordBloodNorway.450k) && 
    require(IlluminaHumanMethylation450kmanifest) && 
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)) {
    sesamized <- sesamize(FlowSorted.CordBloodNorway.450k[,1:2])
  } 

  # reprocess some TCGA 450k data from IDATs 
  if (require(minfi) && 
    require(TCGAMethylation450k) && 
    require(IlluminaHumanMethylation450kmanifest) && 
    require(IlluminaHumanMethylation450kanno.ilmn12.hg19)) {
    TCGA_path <- system.file("extdata","idat", package="TCGAMethylation450k")
    TCGA_IDATs <- list.files(TCGA_path)
    TCGA_stubs <- unique(sub("_(Red|Grn).idat", "", TCGA_IDATs))
    TCGA_targets <- data.frame(Basename=TCGA_stubs)
    TCGA_rgSet <- read.metharray.exp(base=TCGA_path, targets=TCGA_targets)
    TCGA_grSet <- sesamize(TCGA_rgSet)
  }

ttriche/sesamizeGEO documentation built on Nov. 12, 2023, 5:42 p.m.