Hi all,
I have some uncertainties trying to interpret the FDR values from the output table of ImpulseDE2. Let's say I run the following code:
objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = FALSE,
vecConfounders = c("Batch"),
boolIdentifyTransients = TRUE,
scaNProc = 1 )
This would give me an output containing the following key columns:
Gene
p
padj
loglik_full
loglik_red
impulseTOsigmoid_padj
sigmoidTOconst_padj
isTransient
isMonotonous
My question then is, if I want to use a different cutoff to select significant transient
and progression
genes (hence I need to filter the output based on FDR), which padj
column correspond to is.Transient
and is.Monotonous
respectively? Also, does the output table contain information whether this gene is upregulated or downregulated? Thanks in advance.