getPeak2GeneLinks

[eblchen]

Seem to be able to run addPeak2GeneLinks successfully (see log file).
huh6.filt.project <- addPeak2GeneLinks(ArchRProj = huh6.filt.project, useMatrix = "GeneExpressionMatrix", reducedDims = "IterativeLSI")
ArchR-addPeak2GeneLinks-c00f53b28eca-Date-2024-11-28_Time-16-36-36.047589.log

But when I next run getPeak2GeneLinks(), the result is empty:

> peaks.to.gene <- getPeak2GeneLinks(ArchRProj = huh6.filt.project, corCutOff = -10, FDRCutOff = 10, 
                                   varCutOffATAC = 0, varCutOffRNA = 0, resolution = 1, returnLoops = FALSE)
> nrow(peaks.to.gene)
NULL

Or if I try to run with returnLoops = TRUE I get an error:

> peaks.to.gene.granges <- getPeak2GeneLinks(ArchRProj = huh6.filt.project, corCutOff = -10, FDRCutOff = 10, 
+                                            varCutOffATAC = 0, varCutOffRNA = 0, resolution = 1, returnLoops = TRUE)
Error in .validInput(input = start, name = "start", valid = c("integer")) : 
  Input value for 'start' is not a integer, (start = numeric) please supply valid input!
In addition: Warning message:
In min(abs(c(input%%1, input%%1 - 1)), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf

Have checked the peak matrix is there and peak set

> getAvailableMatrices(huh6.filt.project)
[1] "GeneExpressionMatrix" "GeneScoreMatrix"      "PeakMatrix"           "TileMatrix"

> huh6.filt.project@peakSet
GRanges object with 222156 ranges and 3 metadata columns:
           seqnames            ranges strand |       idx        GC         N
              <Rle>         <IRanges>  <Rle> | <integer> <numeric> <numeric>
       [1]     chr1       10021-10335      * |         1    0.5206         0
       [2]     chr1     180653-181068      * |         2    0.5385         0
       [3]     chr1     181306-181578      * |         3    0.7326         0
       [4]     chr1     191306-191581      * |         4    0.6123         0
       [5]     chr1     267871-268084      * |         5    0.5374         0
       ...      ...               ...    ... .       ...       ...       ...
  [222152]    chr22 50743337-50743631      * |      4242    0.6169         0
  [222153]    chr22 50756405-50757380      * |      4243    0.5656         0
  [222154]    chr22 50774898-50775485      * |      4244    0.5544         0
  [222155]    chr22 50780312-50780531      * |      4245    0.4364         0
  [222156]    chr22 50783111-50784106      * |      4246    0.6466         0
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

running info

> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.7.1

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-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

Random number generation:
 RNG:     L'Ecuyer-CMRG 
 Normal:  Inversion 
 Sample:  Rejection 
 
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: Europe/London
tzcode source: internal

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] nabor_0.5.0                 hexbin_1.28.4               viridis_0.6.5               viridisLite_0.4.2           Signac_1.14.0              
 [6] SeuratObject_5.0.2          Seurat_4.4.0                rhdf5_2.46.1                SummarizedExperiment_1.32.0 Biobase_2.62.0             
[11] RcppArmadillo_14.2.0-1      Rcpp_1.0.13-1               Matrix_1.6-5                GenomicRanges_1.54.1        GenomeInfoDb_1.38.8        
[16] IRanges_2.36.0              S4Vectors_0.40.2            BiocGenerics_0.48.1         sparseMatrixStats_1.14.0    MatrixGenerics_1.14.0      
[21] matrixStats_1.4.1           data.table_1.16.2           stringr_1.5.1               plyr_1.8.9                  magrittr_2.0.3             
[26] ggplot2_3.4.2               gtable_0.3.6                gtools_3.9.5                gridExtra_2.3               devtools_2.4.5             
[31] usethis_3.0.0               ArchR_1.0.3                

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22                  splines_4.3.3                     later_1.3.2                       BiocIO_1.12.0                    
  [5] bitops_1.0-9                      tibble_3.2.1                      polyclip_1.10-7                   XML_3.99-0.17                    
  [9] lifecycle_1.0.4                   doParallel_1.0.17                 globals_0.16.3                    lattice_0.22-5                   
 [13] MASS_7.3-60.0.1                   plotly_4.10.4                     yaml_2.3.10                       BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [17] remotes_2.5.0                     httpuv_1.6.15                     sctransform_0.4.1                 spam_2.11-0                      
 [21] sp_2.1-4                          sessioninfo_1.2.2                 pkgbuild_1.4.5                    spatstat.sparse_3.1-0            
 [25] reticulate_1.40.0                 cowplot_1.1.3                     pbapply_1.7-2                     RColorBrewer_1.1-3               
 [29] abind_1.4-8                       pkgload_1.4.0                     zlibbioc_1.48.2                   Rtsne_0.17                       
 [33] purrr_1.0.2                       RCurl_1.98-1.16                   circlize_0.4.16                   GenomeInfoDbData_1.2.11          
 [37] ggrepel_0.9.6                     irlba_2.3.5.1                     listenv_0.9.1                     spatstat.utils_3.1-1             
 [41] goftest_1.2-3                     spatstat.random_3.3-2             fitdistrplus_1.2-1                parallelly_1.39.0                
 [45] RcppRoll_0.3.1                    leiden_0.4.3.1                    codetools_0.2-19                  DelayedArray_0.28.0              
 [49] tidyselect_1.2.1                  shape_1.4.6.1                     farver_2.1.2                      spatstat.explore_3.3-3           
 [53] GenomicAlignments_1.38.2          jsonlite_1.8.9                    GetoptLong_1.0.5                  ellipsis_0.3.2                   
 [57] progressr_0.15.0                  ggridges_0.5.6                    survival_3.5-8                    iterators_1.0.14                 
 [61] foreach_1.5.2                     tools_4.3.3                       ica_1.0-3                         glue_1.8.0                       
 [65] SparseArray_1.2.4                 dplyr_1.1.4                       withr_3.0.2                       BiocManager_1.30.25              
 [69] fastmap_1.2.0                     rhdf5filters_1.14.1               fansi_1.0.6                       digest_0.6.37                    
 [73] R6_2.5.1                          mime_0.12                         colorspace_2.1-1                  Cairo_1.6-2                      
 [77] scattermore_1.2                   tensor_1.5                        spatstat.data_3.1-4               utf8_1.2.4                       
 [81] tidyr_1.3.1                       generics_0.1.3                    renv_1.0.11                       rtracklayer_1.62.0               
 [85] httr_1.4.7                        htmlwidgets_1.6.4                 S4Arrays_1.2.1                    uwot_0.2.2                       
 [89] pkgconfig_2.0.3                   ComplexHeatmap_2.18.0             lmtest_0.9-40                     XVector_0.42.0                   
 [93] htmltools_0.5.8.1                 profvis_0.4.0                     dotCall64_1.2                     clue_0.3-65                      
 [97] scales_1.3.0                      png_0.1-8                         spatstat.univar_3.1-1             rstudioapi_0.17.1                
[101] reshape2_1.4.4                    rjson_0.2.23                      nlme_3.1-164                      cachem_1.1.0                     
[105] zoo_1.8-12                        GlobalOptions_0.1.2               KernSmooth_2.23-22                miniUI_0.1.1.1                   
[109] restfulr_0.0.15                   pillar_1.9.0                      vctrs_0.6.5                       RANN_2.6.2                       
[113] urlchecker_1.0.1                  promises_1.3.0                    xtable_1.8-4                      cluster_2.1.6                    
[117] Rsamtools_2.18.0                  cli_3.6.3                         compiler_4.3.3                    rlang_1.1.4                      
[121] crayon_1.5.3                      future.apply_1.11.3               labeling_0.4.3                    fs_1.6.5                         
[125] stringi_1.8.4                     BiocParallel_1.36.0               deldir_2.0-4                      Biostrings_2.70.3                
[129] munsell_0.5.1                     lazyeval_0.2.2                    spatstat.geom_3.3-3               BSgenome_1.70.2                  
[133] patchwork_1.3.0                   future_1.34.0                     Rhdf5lib_1.24.2                   shiny_1.9.1                      
[137] ROCR_1.0-11                       igraph_2.1.1                      memoise_2.0.1                     fastmatch_1.1-4  

any advice what to try next?

[rcorces]

Hi @eblchen! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.