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dozmorovlab / SpectralTAD

TAD Calling using spectral clustering in R
https://dozmorovlab.github.io/SpectralTAD/
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Error when calling SpectralTAD on the rao contact matrix built into the package #12

Open caragraduate opened 9 months ago

caragraduate commented 9 months ago

Hi there,

Thanks for developing this package. I recently met a new problem as I am working on calling SpectralTAD on the .hic format data, which I can successfully running before but recently it gave me the error below, which also happened when I use the built in rao contact matrix.

Get the rao contact matrix built into the package

data("rao_chr20_25_rep")

results = SpectralTAD(rao_chr20_25_rep, chr = "chr20", resolution = 25000, qual_filter = FALSE, z_clust = FALSE) Converting to n x n matrix Matrix dimensions: 2517x2517 Error in vec_init(): ! x must be a vector, not NULL. Run rlang::last_trace() to see where the error occurred. Warning messages: 1: Unknown or uninitialised column: Group. 2: Unknown or uninitialised column: Group.

I did not have the Group column and could you let me know how should I deal with this Error in vec_init(): ! x must be a vector, not NULL. error? Thank you for your incoming help!

mdozmorov commented 9 months ago

Hi @caragraduate, I'm unable to reproduce. Can you check your R/Bioconductor versions are the latest and all packages are up to date? Here's my sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.2.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SpectralTAD_1.18.0

loaded via a namespace (and not attached):
 [1] utf8_1.2.4                  generics_0.1.3              SparseArray_1.2.2           bitops_1.0-7                gtools_3.9.5                KernSmooth_2.23-22          lattice_0.22-5              magrittr_2.0.3              RColorBrewer_1.1-3          grid_4.3.2                  Matrix_1.6-4                GenomeInfoDb_1.38.1         gridExtra_2.3               mgcv_1.9-0                 
[15] fansi_1.0.6                 HiCcompare_1.24.0           scales_1.3.0                codetools_0.2-19            abind_1.4-5                 cli_3.6.1                   rlang_1.1.2                 crayon_1.5.2                XVector_0.42.0              Biobase_2.62.0              munsell_0.5.0               splines_4.3.2               DelayedArray_0.28.0         S4Arrays_1.2.0             
[29] parallel_4.3.2              tools_4.3.2                 BiocParallel_1.36.0         dplyr_1.1.4                 Rhdf5lib_1.24.1             colorspace_2.1-0            ggplot2_3.4.4               GenomeInfoDbData_1.2.11     InteractionSet_1.30.0       SummarizedExperiment_1.32.0 BiocGenerics_0.48.1         vctrs_0.6.5                 R6_2.5.1                    rhdf5_2.46.1               
[43] matrixStats_1.1.0           stats4_4.3.2                lifecycle_1.0.4             zlibbioc_1.48.0             S4Vectors_0.40.2            IRanges_2.36.0              pkgconfig_2.0.3             pillar_1.9.0                gtable_0.3.4                data.table_1.14.10          glue_1.6.2                  Rcpp_1.0.11                 xfun_0.41                   tibble_3.2.1               
[57] GenomicRanges_1.54.1        tidyselect_1.2.0            rhdf5filters_1.14.1         rstudioapi_0.15.0           MatrixGenerics_1.14.0       knitr_1.45                  nlme_3.1-164                pheatmap_1.0.12             compiler_4.3.2              RCurl_1.98-1.13