SeSAMe-Minfi interaction

SeSAMe can be converted back and forth from Minfi RGChannelSet in multiple ways. One can sesamize a minfi RGChannelSet which returns a GenomicRatioSet. Here we are illustrating using the FlowSorted.Blood.450k object, which is distributed in the minfi::RGChannelSet.

library(sesame)
library(FlowSorted.Blood.450k)

grSet <- sesamize(FlowSorted.Blood.450k[,1:4])

## Sesamizing WB_105...

## Sesamizing WB_218...

## Sesamizing WB_261...

## Sesamizing PBMC_105...

## Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19

## Loading required package: IlluminaHumanMethylation450kmanifest

grSet

## class: GenomicRatioSet 
## dim: 485512 4 
## metadata(1): SNPs
## assays(2): Beta CN
## rownames(485512): cg13869341 cg14008030 ... cg08265308 cg14273923
## rowData names(0):
## colnames(4): WB_105 WB_218 WB_261 PBMC_105
## colData names(8): Sample_Name Slide ... CellType Sex
## Annotation
##   array: IlluminaHumanMethylation450k
##   annotation: ilmn12.hg19
## Preprocessing
##   Method: SeSAMe (type I)
##   minfi version: 1.32.0
##   Manifest version: 0.6.0