Hello,
I get the following error when trying to run FindIntegrationAnchors on a few scATAC-seq datasets run through Signac.
Error in names(cells) <- new.names[names(x = cells)] :
attempt to set an attribute on NULL
In addition: Warning message:
In CheckDuplicateCellNames(object.list = object.list) :
Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.
Here is the relevant code leading up to this error. seu is a list of scATAC-seq Seurat objects and frags is a list of Fragment Objects.
library("Signac")
library("Seurat")
library("tidyverse")
## Get unified (reduced) peaks.
unified_peaks <- UnifyPeaks(seu)
## For each sample get a new count matrix using the unified peaks.
mats <- map(frags, FeatureMatrix, unified_peaks)
# Filter out cells that aren't in the original seurat object.
mats <- map2(mats, seu, ~`[`(.x, , colnames(.x) %in% colnames(.y)))
## Create chromatin assays and seurat objects for unified peaks.
seu_unif <- mats %>%
map2(frags, ~CreateChromatinAssay(.x, fragments=.y, annotation=anno)) %>%
imap(~CreateSeuratObject(.x, project=.y, assay="ATAC"))
## Normalization.
seu_unif <- map(seu_unif, RunTFIDF)
## Find integration anchors.
anchors <- FindIntegrationAnchors(seu_unif, reduction="rlsi", dims=2:30)
Here is my session info.
R version 4.1.0 (2021-05-18)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /software/miniconda3/envs/singlecell/lib/libopenblasp-r0.3.15.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.44.0 AnnotationDbi_1.54.0
[3] clustree_0.4.3 ggraph_2.0.5
[5] ggrastr_0.2.3 scDblFinder_1.6.0
[7] SingleCellExperiment_1.14.1 SummarizedExperiment_1.22.0
[9] Biobase_2.52.0 MatrixGenerics_1.4.0
[11] matrixStats_0.59.0 SeuratObject_4.0.2
[13] Seurat_4.0.3 rtracklayer_1.52.0
[15] GenomicRanges_1.44.0 GenomeInfoDb_1.28.0
[17] IRanges_2.26.0 S4Vectors_0.30.0
[19] BiocGenerics_0.38.0 future_1.21.0
[21] patchwork_1.1.1 forcats_0.5.1
[23] stringr_1.4.0 dplyr_1.0.7
[25] purrr_0.3.4 readr_1.4.0
[27] tidyr_1.1.3 tibble_3.1.2
[29] ggplot2_3.3.5 tidyverse_1.3.1
[31] Signac_1.2.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 SnowballC_0.7.0
[3] scattermore_0.7 bit64_4.0.5
[5] irlba_2.3.3 DelayedArray_0.18.0
[7] data.table_1.14.0 rpart_4.1-15
[9] KEGGREST_1.32.0 RCurl_1.98-1.3
[11] generics_0.1.0 ScaledMatrix_1.0.0
[13] cowplot_1.1.1 RSQLite_2.2.5
[15] RANN_2.6.1 bit_4.0.4
[17] spatstat.data_2.1-0 xml2_1.3.2
[19] lubridate_1.7.10 httpuv_1.6.1
[21] assertthat_0.2.1 viridis_0.6.1
[23] hms_1.1.0 promises_1.2.0.1
[25] fansi_0.4.2 restfulr_0.0.13
[27] progress_1.2.2 dbplyr_2.1.1
[29] readxl_1.3.1 igraph_1.2.6
[31] DBI_1.1.1 htmlwidgets_1.5.3
[33] sparsesvd_0.2 spatstat.geom_2.2-0
[35] ellipsis_0.3.2 backports_1.2.1
[37] biomaRt_2.48.0 deldir_0.2-10
[39] sparseMatrixStats_1.4.0 vctrs_0.3.8
[41] ROCR_1.0-11 abind_1.4-5
[43] cachem_1.0.5 withr_2.4.2
[45] ggforce_0.3.3 sctransform_0.3.2
[47] GenomicAlignments_1.28.0 prettyunits_1.1.1
[49] scran_1.20.1 goftest_1.2-2
[51] cluster_2.1.2 lazyeval_0.2.2
[53] crayon_1.4.1 edgeR_3.34.0
[55] pkgconfig_2.0.3 slam_0.1-48
[57] tweenr_1.0.2 nlme_3.1-152
[59] vipor_0.4.5 rlang_0.4.11
[61] globals_0.14.0 lifecycle_1.0.0
[63] miniUI_0.1.1.1 filelock_1.0.2
[65] BiocFileCache_2.0.0 modelr_0.1.8
[67] rsvd_1.0.5 cellranger_1.1.0
[69] polyclip_1.10-0 lmtest_0.9-38
[71] Matrix_1.3-4 ggseqlogo_0.1
[73] zoo_1.8-9 reprex_2.0.0
[75] beeswarm_0.4.0 ggridges_0.5.3
[77] png_0.1-7 viridisLite_0.4.0
[79] rjson_0.2.20 bitops_1.0-7
[81] KernSmooth_2.23-20 Biostrings_2.60.0
[83] blob_1.2.1 DelayedMatrixStats_1.14.0
[85] parallelly_1.26.1 beachmat_2.8.0
[87] scales_1.1.1 memoise_2.0.0
[89] magrittr_2.0.1 plyr_1.8.6
[91] ica_1.0-2 zlibbioc_1.38.0
[93] compiler_4.1.0 dqrng_0.3.0
[95] BiocIO_1.2.0 RColorBrewer_1.1-2
[97] fitdistrplus_1.1-5 Rsamtools_2.8.0
[99] cli_3.0.0 XVector_0.32.0
[101] listenv_0.8.0 pbapply_1.4-3
[103] MASS_7.3-54 mgcv_1.8-36
[105] tidyselect_1.1.1 stringi_1.6.2
[107] yaml_2.2.1 BiocSingular_1.8.0
[109] locfit_1.5-9.4 ggrepel_0.9.1
[111] grid_4.1.0 fastmatch_1.1-0
[113] tools_4.1.0 future.apply_1.7.0
[115] rstudioapi_0.13 bluster_1.2.1
[117] lsa_0.73.2 metapod_1.0.0
[119] gridExtra_2.3 farver_2.1.0
[121] Rtsne_0.15 digest_0.6.27
[123] shiny_1.6.0 qlcMatrix_0.9.7
[125] Rcpp_1.0.7 broom_0.7.8
[127] scuttle_1.2.0 later_1.2.0
[129] RcppAnnoy_0.0.18 httr_1.4.2
[131] colorspace_2.0-2 rvest_1.0.0
[133] XML_3.99-0.6 fs_1.5.0
[135] tensor_1.5 reticulate_1.20
[137] splines_4.1.0 uwot_0.1.10
[139] RcppRoll_0.3.0 statmod_1.4.36
[141] spatstat.utils_2.2-0 scater_1.20.0
[143] graphlayouts_0.7.1 xgboost_1.4.0.1
[145] plotly_4.9.4.1 xtable_1.8-4
[147] jsonlite_1.7.2 tidygraph_1.2.0
[149] R6_2.5.0 pillar_1.6.1
[151] htmltools_0.5.1.1 mime_0.11
[153] glue_1.4.2 fastmap_1.1.0
[155] BiocParallel_1.26.0 BiocNeighbors_1.10.0
[157] codetools_0.2-18 utf8_1.2.1
[159] lattice_0.20-44 spatstat.sparse_2.0-0
[161] curl_4.3.2 ggbeeswarm_0.6.0
[163] leiden_0.3.8 survival_3.2-11
[165] limma_3.48.0 docopt_0.7.1
[167] munsell_0.5.0 GenomeInfoDbData_1.2.6
[169] haven_2.4.1 reshape2_1.4.4
[171] gtable_0.3.0 spatstat.core_2.2-0
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4