Suppose I have run deseq like this:
my_coldata$varA = factor(mycoldata$varA, levels=c('control', 'case') my_coldata$varB = factor(mycoldata$varB, levels=c(0,1)) dds = DESeqDataSetFromMatrix( countData=my_counts, colData=my_coldata, design=~varA + varB ) deseq_obj = DESeq( dds, test='Wald', fitType='mean' )
I can access the metadata with
colData(deseq_obj) but it comes as a matrix with factor and level information wiped out. Is there a way to access this information?
Maybe a suggestion would be to switch to DataFrames since that is becoming ever more standard in the r-verse.