Is there a way to get DEG results from a specific subset of comparisons without subsetting the samples prior to running the DESeq model?
I'm working with an RNAseq dataset that came from an experiment with a multifactorial design: two timepoints, two temperatures, and two drugs. The full model and contrasts give me the following list of results:
dds <- DESeqDataSetFromMatrix(gcounts, colData = colData,
design = formula(~ drug * temp * timepoint))
ddsR <- DESeq(dds, minReplicatesForReplace = Inf)
res <- results(ddsR, contrast = c(0, 1, 0, 0, 0, 0, 0, 0)) #example
#[1] "Intercept"
#[2] "drug_B_vs_A"
#[3] "temp_18_vs_14"
#[4] "timepoint_24h_vs_0h"
#[5] "drugB.temp18"
#[6] "drugB.timepoint24h"
#[7] "temp18.timepoint24h"
#[8] "drugB.temp18.timepoint24hpi"
I'm trying to understand whether there's a way to get results like: a comparison of DEGs in temp18 and temp14 at 0h only, irrespective of their differences at 24h. 0h is currently set as the baseline for this factor.
Is there a way to do that by using the results(ddss, contrast = (x,x,x,x,x,x)) line? (some combination of 0, 1, and -1?) Or would I need to subset samples and run models on those smaller sample sets?
