Question

Error with regionCounts()

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Chris ▴ 20

@3fdb6f97

Last seen 4 months ago

United States

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!

csaw • 1.3k views

ADD COMMENT • link 20 months ago Chris ▴ 20

score 1 · Answer 1 · 2023-04-03

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ATpoint ★ 4.6k

@atpoint-13662

Last seen 1 hour ago

Germany

Googling 'position vector should be one-based'

https://www.biostars.org/p/9541255/#9541272

ADD COMMENT • link 20 months ago ATpoint ★ 4.6k

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Thanks ATpoint for your help. I read your biostars link and applied your code but got this:

start(all.peaks) <- start(all.peaks) + 1

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?

ADD REPLY • link 20 months ago Chris ▴ 20

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What is class(all.peaks). This works for GRanges objects.

library(GenomicRanges)

gr <- GRanges(seqnames=c("chr1", "chr2"),
              ranges=IRanges(start=c(0,1), end=c(5,6)))

start(gr) <- start(gr)+1

Maybe some namespace conflict, try also GenomicRanges::start().

ADD REPLY • link 20 months ago ATpoint ★ 4.6k

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ATpoint Thank you for your help!

class(all.peaks)

[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

Don't know why start(gr) <- start(gr)+1 doesn't have error anymore but still:

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

ADD REPLY • link 20 months ago Chris ▴ 20