I'm very new to TCGAbiolinks and I'm running through their given case studies in this link. I'm running case study 3, which is "Case study n. 3: Integration of methylation and expression for ACC" and as I'm running through the given code blocks, it's giving me an error and will not produce a volcano plot.
The first error was that there was an extra parenthesis in the na.omit line. I figured that as it was able to produce a figure in the case study, it would work but it didn't so I tried to take it out and the line did work. However, after that, when I run the code under #Volcano plot, it tells me that there is no "subtype_MethyLevel" in my data. I looked at it myself and it seemed that the tsv data didn't have a column and maybe that was why? But I'm not really sure how to fix it so that the code will be able to produce a volcano plot as shown in the link. Does anyone have any solution for me? Thank you for your time!
# na.omit acc.met <- acc.met[rowSums(is.na(assay(acc.met))) == 0),] # Volcano plot acc.met <- TCGAanalyze_DMC( data = acc.met, groupCol = "subtype_MethyLevel", group1 = "CIMP-high", group2="CIMP-low", p.cut = 10^-5, diffmean.cut = 0.25, legend = "State", plot.filename = "CIMP-highvsCIMP-low_metvolcano.png" )