I am trying to perform DGE analysis with Deseq2 in python using the rpy2 package. I have currently managed to reach the step where I have my results in the RS4 object format. Ideally now I would like to save myresults in a .csv. The myresults is a type rpy2.robjects.methods.RS4.
myresults = deseq2.results(dds)
print(myresults)
log2 fold change (MLE): treatment untreated vs treated
Wald test p-value: treatment untreated vs treated
DataFrame with 25958 rows and 6 columns
baseMean log2FoldChange lfcSE stat pvalue padj
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
A1BG 140.51466 -0.832851 0.571502 -1.457303 0.1450326 0.713127
A1CF 4.14679 -0.191442 1.093415 -0.175086 0.8610119 0.966298
I tried to find my way through myresults.slots() with the purpose of retrieving the count matrix, colnames, rownames and merging them into a python data frame that can I easily save as a .csv. I am still unable to extract useful things.
items = list(result.slots.items())
items[0]
keyss = list(result.slots.keys())
keyss[0]
Since I am vastly unfamiliar with the structure of RS4 objects it still confuses me and takes too much time. Any help in that direction or a solution would be greatly appreciated! :)