Entering edit mode
Hi all,
Would you have a suggestion how to fix this error?
peak.counts <- regionCounts(pe.bams, all.peaks, param=param)
Error: BiocParallel errors
1 remote errors, element index: 1 3 unevaluated and other errors first remote error: Error: position vector should be 1-based
I found a similar error here:
BiocParallel error with ChIPQC
Thank you so much!
Thanks ATpoint for your help. I read your biostars link and applied your code but got this:
Error in attr(x, "tsp") <- c(1, NROW(x), 1) : invalid time series parameters specified
The guys in the post figured out the solution but I still don't know how. Would you have a suggestion?
What is
class(all.peaks)
. This works for GRanges objects.Maybe some namespace conflict, try also
GenomicRanges::start()
.ATpoint Thank you for your help!
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
Don't know why
start(gr) <- start(gr)+1
doesn't have error anymore but still:Error: BiocParallel errors 1 remote errors, element index: 1
3 unevaluated and other errors
first remote error:
Error: position vector should be 1-based