Hello, I was running the RU_ATAC_Workshop and found an error at the step which calls this function. I have run the following code:
peaks <- dir("./ATAC_Data/ATAC_Peaks_forCounting/", pattern = "*.narrowPeak",
full.names = TRUE)
myPeaks <- lapply(peaks, ChIPQC:::GetGRanges, simple = TRUE)
names(myPeaks) <- c("HindBrain_1", "HindBrain_2", "Kidney_1", "Kidney_2", "Liver_1",
"Liver_2")
Group <- factor(c("HindBrain", "HindBrain", "Kidney", "Kidney", "Liver", "Liver"))
consensusToCount <- runConsensusRegions(GRangesList(myPeaks), "none")
The function "runConsensusRegions" returns the variable "consensusToCount" as NULL in the workflow. It looks like the issue is that the function expects the input to be a "GRangesList" however the input as directed by the workflow of GRangesList(myPeaks) is of class "CompressedGRangesList". Because the class is wrong that seems to be why it is returning NULL.
soGGi/R/peakTransforms.r
Line 118 in 5f9d323
Hello, I was running the RU_ATAC_Workshop and found an error at the step which calls this function. I have run the following code:
The function "runConsensusRegions" returns the variable "consensusToCount" as NULL in the workflow. It looks like the issue is that the function expects the input to be a "GRangesList" however the input as directed by the workflow of GRangesList(myPeaks) is of class "CompressedGRangesList". Because the class is wrong that seems to be why it is returning NULL.