How to extract the results table for specific samples names after normalization by DESeq in R?
After I did normalization in R with DESeq2 I got the results table with results function, now I need to get the results but not for all samples, I just need for 2 samples, how to extract it?
res <- results(dds)
res
log2 fold change (MLE): condition Normal Cell vs Cancer Cell
Thanks in advance
I guess the best solution for this question is:
countdata3<- subset(countdata, select=c("sample_name1_rep1", "sample_name1_rep2", sample_name2_rep1","sample_name2_rep2"))
coldata3<- data.frame("condition"=as.factor(c(rep("Normal",2),rep("Mutated",2))),row.names=colnames(countdata3))
dds3 <- DESeqDataSetFromMatrix(countData = countdata3, colData =coldata3,design = ~condition )
dds3 <- DESeq(dds3)
results(dds3)
Then the results will be calculated depending on the samples inside the dataframe not all samples.
How to extract the results table for specific samples
You are not "extracting" the result table. You are doing a completely new the deseq2 analysis with a smaller set of samples from the original dataframe (countdata)
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