GreenleafLab
getPeak2GeneLinks
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?
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.
