I've been able to create a summarized experiment but I'm having some difficulty subsetting and expressing my data. For example, I have arranged my summarizedexperiment by gene with RNA-seq (seq) and methylation data (methyl) See example code:
seq <- data.frame("GAPDH" = c(1,5,NA, NA), "ACTB" = c(10,15, NA, NA))
methyl <- data.frame("GAPDH" = c(10,20,0,0), "ACTB" = c(0,0,50,100))
A = SummarizedExperiment(assays=list(seq,methyl))
what I'd like to be able to do next is to pull both the seq and methyl data for "GAPDH".
I realize that this is probably simple but I've looked over the subsetting section and am still have some difficulty figuring it out.