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GreenleafLab
chromVAR computeDeviations error:Error in isVirtualExt(exti) :
Hello, when I was running computeDeviations in the following code, an error occurred:
dev <- computeDeviations(object = rse, annotations = motif_mm); Error in isVirtualExt(exti) : trying to get slot "virtual" from an object of a basic class ("NULL") with no slots
Below is the traceback():
traceback() 17: stop(e) 16: value[3L] 15: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14: tryCatchList(expr, classes, parentenv, handlers) 13: tryCatch({ FUN(...) }, error = handle_error) 12: withCallingHandlers({ tryCatch({ FUN(...) }, error = handle_error) }, warning = handle_warning) 11: FUN(...) 10: FUN(X[[i]], ...) 9: lapply(X, FUN_, ...) 8: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM) 6: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 5: bplapply(peak_indices, compute_deviations_single, counts_mat = counts_mat, background_peaks = background_peaks, expectation = expectation) 4: compute_deviations_core(counts(object), peak_indices, background_peaks, expectation, colData = colData(object), rowData = colData(annotations)) 3: .local(object, annotations, ...) 2: computeDeviations(object = rse, annotations = motif_mm) 1: computeDeviations(object = rse, annotations = motif_mm)
Below is the session info:
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
[1] JASPAR2016_1.16.0 GO.db_3.11.4
[3] AnnotationDbi_1.50.3 chromVARmotifs_0.2.0
[5] ggplot2_3.3.2 viridisLite_0.3.0
[7] BiocParallel_1.22.0 BSgenome.Mmusculus.UCSC.mm10_1.4.0
[9] BSgenome_1.56.0 rtracklayer_1.48.0
[11] Biostrings_2.56.0 XVector_0.28.0
[13] SummarizedExperiment_1.18.2 DelayedArray_0.14.1
[15] matrixStats_0.57.0 Biobase_2.48.0
[17] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2
[19] IRanges_2.22.2 S4Vectors_0.26.1
[21] BiocGenerics_0.34.0 motifmatchr_1.1.1
[23] chromVAR_1.10.0 SnapATAC_1.0.0
[25] rhdf5_2.32.4 Matrix_1.2-18
[27] TFBSTools_1.26.0
Anxiously waiting for feedback！ Thanks, ZHAOLIYANG
Hi liyang,
Did you encounter the error when using the function 'addDeviationsMatrix' of ArchR (ref link: https://www.archrproject.com/bookdown/motif-deviations.html). I have re-run my script in a different working directory (regenerate my arrow files) and I didn't encounter the error again.
Best, Changliang.
发件人: zhaoliyang0429 [email protected] 发送时间: 2020年11月12日 17:14 收件人: GreenleafLab/chromVAR [email protected] 抄送: Wang Changliang [email protected]; Comment [email protected] 主题: Re: [GreenleafLab/chromVAR] chromVAR computeDeviations error:Error in isVirtualExt(exti) : (#82)
not yet
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No I didn't. In ArchR, this function was run successfuIly, I met this error in the snapATAC runChromVAR
https://github.com/r3fang/SnapATAC/issues/211
I also run this function in ArchR and get this error message, How Can I slove this problem,,,, help thanks
