I have EPIC data from 8 samples.
Sample sheet: Sorry I am new to posting here, so please forgive my bad formatting:
Plate Bead chip # Well Position Well Position Sentrix_ID Array Complete Barcode Sample_Name 1447 1 A01 01A 201172520042 R01C01 201172520042_R01C01 MCF10A N 2d 1447 1 B01 01B 201172520042 R02C01 201172520042_R02C01 MCF10A H 0.5% 2d 1447 1 C01 01C 201172520042 R03C01 201172520042_R03C01 68 N 2d 1447 1 D01 01D 201172520042 R04C01 201172520042_R04C01 68 H 4% 2d 1447 1 E01 01E 201172520042 R05C01 201172520042_R05C01 68 H 0.5% 2d 1447 1 F01 01F 201172520042 R06C01 201172520042_R06C01 68 N 8 wk 1447 1 G01 01G 201172520042 R07C01 201172520042_R07C01 68 N 3d 1447 1 H01 01H 201172520042 R08C01 201172520042_R08C01 68 H 4% 8wk
I am trying to find DMPs from the samples N 8 wk and H 4% 8wk. I did the following for normalizing and processing:
setwd("~/Desktop/HYPNOR/") baseDir <- file.path("~/Desktop/HYPNOR/") list.files(file.path(baseDir, "201172520042")) list.files(file.path(baseDir)) targets <- read.metharray.sheet(baseDir) RGset <- read.metharray.exp(targets = targets) RGset phenoData <- pData(RGset) phenoData[,1:6] pd <- pData(RGset) pd pd[,1:4] qcReport(RGset, sampNames = pd$Sample_Name, pdf = "qcReport.pdf") #Preprocessing/Normalizing/DYE correction noob <- preprocessNoob(RGset) RGset GMset_map <- mapToGenome(noob) snp_add <- addSnpInfo(GMset_map) remove_snps <- dropLociWithSnps(snp_add, snps=c("SBE","CpG"), maf=0.05) dmpFinder(remove_snps, pheno = pd$Sample_Group, type = c("categorical"))
What I have tried hasn't worked and I don't know how to single those two samples only for dmpfinder. I made a new sample sheet with just the two samples, but that didn't work and also created a subset of the data, and that didn't work.
I was wondering if there is a better solution for this? I am quite new to EPIC methylation analysis, so my apologies if I sound naive.
Any help would be awesome, please. Thank you.