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.
Thanks! Naming is something that I'm working on! If you have a quick answer for that I'd appreciate it otherwise that I'm pretty sure I can find in the vignette etc.