ArchR
ArchR copied to clipboard
Published
20 hours ago •
GreenleafLab
GreenleafLab
Error Report - addGeneIntegrationMatrix()-Attempting to add a different number of cells and/or features
Hi,
I also occurred similar problem. The seRNA is a seurat object. The column name of seRNA@assays$RNA@counts is different from archrproject$Cellnames. I modifies the name by following code:
seRNA_2 <- readRDS("scRNA_Seurat.RDS")
counts <- GetAssayData(seRNA_2, assay = "RNA",slot = "counts")
seuratRNA_rownames <- colnames(counts)
seuratRNA_rownames[-length(seuratRNA_rownames)] <- paste0(seuratRNA_rownames[-length(seuratRNA_rownames)], '-1')
colnames(counts) <- seuratRNA_rownames
seuratRNA_2 <- CreateSeuratObject(
counts = counts,
meta.data = [email protected]
)
Since the gene name from gene scores matrix (ArchR) is different from rna matrix (seuratRNA_2). I changed the ENSEMBL ID to NCBI ID in rna matrix (seuratRNA_2). There are NAs
seuratRNA_2_ENSEMBL <- rownames(seuratRNA_2)
seuratRNA_2_annots <- mapIds(org.Hs.eg.db, keys = seuratRNA_2_ENSEMBL,
column = c('ENTREZID'), keytype = 'ENSEMBL')
rownames(seuratRNA_2@assays$RNA@counts) <- seuratRNA_2_annots
Then I added geneintegrationmatrix to the archr project (projCCD). However, I got the same error message "Error: Attempting to add a different number of cells and/or features"
projCCD <- addGeneIntegrationMatrix(
ArchRProj = projCCD,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "IterativeLSI",
seRNA = seuratRNA_2,
addToArrow = FALSE,
force = TRUE,
verbose = FALSE,
groupRNA = "seurat_clusters",
nameCell = "predictedCell_Un",
nameGroup = "predictedGroup_Un",
nameScore = "predictedScore_Un"
)
Below is the logFile:
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Logging With ArchR!
Start Time : 2023-09-22 12:24:48.640335
------- ArchR Info
ArchRThreads = 30
ArchRGenome = Hg38
------- System Info
Computer OS = unix
Total Cores = 32
------- Session Info
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: AlmaLinux 8.8 (Sapphire Caracal)
Matrix products: default
BLAS: /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRblas.so
LAPACK: /share/pkg.8/r/4.3.1/install/lib64/R/lib/libRlapack.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] biomaRt_2.56.1 TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0
[3] GenomicFeatures_1.52.1 gridExtra_2.3
[5] uwot_0.1.16 nabor_0.5.0
[7] harmony_1.0.1 Rcpp_1.0.11
[9] ArchR_1.0.0 rhdf5_2.44.0
[11] data.table_1.14.8 SeuratObject_4.9.9.9091
[13] Seurat_4.3.0.1 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[15] BSgenome_1.68.0 rtracklayer_1.60.1
[17] Biostrings_2.68.1 XVector_0.40.0
[19] TFBSTools_1.38.0 JASPAR2018_1.1.1
[21] motifmatchr_1.22.0 GenomicInteractions_1.34.0
[23] InteractionSet_1.28.1 SingleCellExperiment_1.22.0
[25] SummarizedExperiment_1.30.2 GenomicRanges_1.52.0
[27] GenomeInfoDb_1.36.3 MatrixGenerics_1.12.3
[29] matrixStats_1.0.0 clusterProfiler_4.8.3
[31] org.Hs.eg.db_3.17.0 AnnotationDbi_1.62.2
[33] IRanges_2.34.1 S4Vectors_0.38.1
[35] Biobase_2.60.0 BiocGenerics_0.46.0
[37] fclust_2.1.1.1 e1071_1.7-13
[39] Matrix_1.6-0 tibbletime_0.1.8
[41] binr_1.1.1 broom_1.0.5
[43] splitstackshape_1.4.8 reshape2_1.4.4
[45] magrittr_2.0.3 lubridate_1.9.2
[47] forcats_1.0.0 stringr_1.5.0
[49] purrr_1.0.2 readr_2.1.4
[51] tidyr_1.3.0 tibble_3.2.1
[53] tidyverse_2.0.0 dplyr_1.1.3
[55] gghighlight_0.4.0 ggthemes_4.2.4
[57] ggdendro_0.1.23 ggrastr_1.0.2
[59] ggrepel_0.9.3 ggplot2_3.4.3
[61] gplots_3.1.3 patchwork_1.1.3
[63] ComplexHeatmap_2.16.0 circlize_0.4.15
[65] RColorBrewer_1.1-3 wesanderson_0.3.6
[67] viridis_0.6.4 viridisLite_0.4.2
loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 dichromat_2.0-1 progress_1.2.2
[4] urlchecker_1.0.1 nnet_7.3-19 poweRlaw_0.70.6
[7] goftest_1.2-3 vctrs_0.6.3 spatstat.random_3.1-6
[10] digest_0.6.33 png_0.1-8 shape_1.4.6
[13] proxy_0.4-27 parallelly_1.36.0 deldir_1.0-9
[16] MASS_7.3-60 httpuv_1.6.11 foreach_1.5.2
[19] qvalue_2.32.0 withr_2.5.0 xfun_0.40
[22] ggfun_0.1.3 survival_3.5-5 ellipsis_0.3.2
[25] memoise_2.0.1 ggbeeswarm_0.7.2 gson_0.1.0
[28] profvis_0.3.8 zoo_1.8-13 tidytree_0.4.2
[31] GlobalOptions_0.1.2 gtools_3.9.4 pbapply_1.7-2
[34] R.oo_1.25.0 Formula_1.2-6 prettyunits_1.1.1
[37] KEGGREST_1.40.0 promises_1.2.1 httr_1.4.7
[40] downloader_0.4 restfulr_0.0.15 rhdf5filters_1.12.1
[43] fitdistrplus_1.1-11 globals_0.16.2 ps_1.7.5
[46] rstudioapi_0.15.0 miniUI_0.1.1.1 generics_0.1.3
[49] DOSE_3.26.1 base64enc_0.1-3 processx_3.8.1
[52] curl_5.0.2 zlibbioc_1.46.0 ggraph_2.1.0
[55] polyclip_1.10-4 GenomeInfoDbData_1.2.10 xtable_1.8-6
[58] desc_1.4.2 pracma_2.4.2 doParallel_1.0.17
[61] evaluate_0.21 S4Arrays_1.0.6 BiocFileCache_2.8.0
[64] hms_1.1.3 irlba_2.3.5.1 colorspace_2.1-1
[67] filelock_1.0.2 ROCR_1.0-11 spatstat.data_3.0-1
[70] reticulate_1.32.0 lmtest_0.9-40 later_1.3.1
[73] ggtree_3.8.0 lattice_0.21-8 spatstat.geom_3.2-5
[76] future.apply_1.11.0 scattermore_1.2 XML_3.99-0.14
[79] shadowtext_0.1.2 cowplot_1.1.1 RcppAnnoy_0.0.21
[82] class_7.3-22 Hmisc_5.1-0 pillar_1.9.0
[85] nlme_3.1-162 iterators_1.0.14 caTools_1.18.2
[88] compiler_4.3.1 stringi_1.7.12 tensor_1.5
[91] devtools_2.4.5 GenomicAlignments_1.36.0 plyr_1.8.8
[94] crayon_1.5.2 abind_1.4-7 BiocIO_1.10.0
[97] gridGraphics_0.5-1 sp_2.0-0 graphlayouts_1.0.0
[100] bit_4.0.5 fastmatch_1.1-4 codetools_0.2-19
[103] biovizBase_1.48.0 GetoptLong_1.0.5 plotly_4.10.2
[106] mime_0.12 splines_4.3.1 dbplyr_2.3.2
[109] HDO.db_0.99.1 interp_1.1-4 knitr_1.44
[112] blob_1.2.4 utf8_1.2.3 clue_0.3-64
[115] seqLogo_1.66.0 AnnotationFilter_1.24.0 fs_1.6.3
[118] listenv_0.9.0 checkmate_2.2.0 pkgbuild_1.4.1
[121] Gviz_1.44.1 ggplotify_0.1.2 callr_3.7.3
[124] tzdb_0.4.0 tweenr_2.0.2 pkgconfig_2.0.3
[127] tools_4.3.1 cachem_1.0.8 RhpcBLASctl_0.23-42
[130] RSQLite_2.3.1 DBI_1.1.3 fastmap_1.1.1
[133] rmarkdown_2.25 scales_1.2.1 usethis_2.2.0
[136] ica_1.0-3 Rsamtools_2.16.0 BiocManager_1.30.21
[139] dotCall64_1.0-2 VariantAnnotation_1.46.0 RANN_2.6.1
[142] rpart_4.1.19 farver_2.1.1 tidygraph_1.2.3
[145] scatterpie_0.2.1 yaml_2.3.7 latticeExtra_0.6-30
[148] foreign_0.8-84 cli_3.6.1 leiden_0.4.3
[151] lifecycle_1.0.3 sessioninfo_1.2.2 backports_1.4.1
[154] BiocParallel_1.34.2 annotate_1.78.0 timechange_0.2.0
[157] gtable_0.3.4 rjson_0.2.21 ggridges_0.5.4
[160] progressr_0.14.0 ape_5.7-1 jsonlite_1.8.7
[163] bitops_1.0-7 bit64_4.0.5 Rtsne_0.16
[166] yulab.utils_0.1.0 spatstat.utils_3.0-3 CNEr_1.36.0
[169] GOSemSim_2.26.1 R.utils_2.12.2 lazyeval_0.2.2
[172] shiny_1.7.5 htmltools_0.5.6 enrichplot_1.20.3
[175] sctransform_0.3.5 GO.db_3.17.0 rappdirs_0.3.3
[178] ensembldb_2.24.0 glue_1.6.2 TFMPvalue_0.0.9
[181] spam_2.9-1 RCurl_1.98-1.12 rprojroot_2.0.3
[184] treeio_1.24.1 jpeg_0.1-10 igraph_1.5.1
[187] R6_2.5.1 labeling_0.4.3 cluster_2.1.4
[190] Rhdf5lib_1.22.1 pkgload_1.3.2 aplot_0.2.1
[193] DirichletMultinomial_1.42.0 DelayedArray_0.26.7 tidyselect_1.2.0
[196] vipor_0.4.5 ProtGenerics_1.32.0 htmlTable_2.4.1
[199] ggforce_0.4.1 xml2_1.3.4 future_1.33.0
[202] munsell_0.5.0 KernSmooth_2.23-21 htmlwidgets_1.6.2
[205] fgsea_1.26.0 spatstat.sparse_3.0-2 rlang_1.1.1
[208] spatstat.explore_3.2-3 remotes_2.4.2 Cairo_1.6-0
[211] fansi_1.0.4 beeswarm_0.4.0
------- Log Info
2023-09-22 12:24:49.022809 : Running Seurat's Integration Stuart* et al 2019, 0.006 mins elapsed.
2023-09-22 12:24:49.031734 : Input-Parameters, Class = list
Input-Parameters$: length = 1
1 function (name)
2 .Internal(args(name))
Input-Parameters$ArchRProj: length = 1
Input-Parameters$useMatrix: length = 1
[1] "GeneScoreMatrix"
Input-Parameters$matrixName: length = 1
[1] "GeneIntegrationMatrix"
Input-Parameters$reducedDims: length = 1
[1] "IterativeLSI"
Input-Parameters$seRNA: length = 1
orig.ident nCount_RNA nFeature_RNA sample_sampleId_short
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 hft 1397 677 <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 hft 14338 4301 <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 hft 9260 3481 <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 hft 4025 1969 <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 hft 7131 2930 <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 hft 6532 2712 <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 hft 8764 3642 <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 hft 953 523 <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 hft 2382 1087 <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 hft 5857 2500 <NA>
sample_name_at sample_time sample_cellLine
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 <NA> <NA> <NA>
sample_sampleType sample_diseaseType
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 <NA> <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 <NA> <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 <NA> <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 <NA> <NA>
sample_differentiation sample_assay sample_batch
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 <NA> <NA> <NA>
sample_barcode sample_barcodeName sample_seqrunDir
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 <NA> <NA> <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 <NA> <NA> <NA>
percentMT percentRibo cell_barcode
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA <NA>
CR_Estimated.Number.of.Cells CR_Mean.Reads.per.Cell
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Median.Genes.per.Cell CR_Number.of.Reads
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Valid.Barcodes CR_Sequencing.Saturation
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Q30.Bases.in.Barcode CR_Q30.Bases.in.RNA.Read
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Q30.Bases.in.Sample.Index CR_Q30.Bases.in.UMI
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Reads.Mapped.to.Genome
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Confidently.to.Genome
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Confidently.to.Intergenic.Regions
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Confidently.to.Intronic.Regions
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Confidently.to.Exonic.Regions
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Confidently.to.Transcriptome
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Reads.Mapped.Antisense.to.Gene
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA
CR_Fraction.Reads.in.Cells CR_Total.Genes.Detected
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA
CR_Median.UMI.Counts.per.Cell DF_pANN DF_classification
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA <NA>
DF_pANN_quantile nCount_spliced nFeature_spliced
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA NA
nCount_unspliced nFeature_unspliced nCount_ambiguous
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA NA NA
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA NA NA
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA NA NA
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA NA NA
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA NA NA
nFeature_ambiguous RNA_snn_res.0.5 seurat_clusters
hft_w20_p3_r1_AAACCCAAGCTGCGAA-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAAGGTAGTAT-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCACAACTCCAA-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCACATAGTCAC-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACAGGTG-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACGGTTT-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTACTCGCG-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTATGTCCA-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTGTATTCG-1 NA <NA> <NA>
hft_w20_p3_r1_AAACCCAGTTGCTCAA-1 NA <NA> <NA>
Input-Parameters$groupATAC: length = 0
NULL
Input-Parameters$groupRNA: length = 1
[1] "seurat_clusters"
Input-Parameters$groupList: length = 0
NULL
Input-Parameters$sampleCellsATAC: length = 1
[1] 10000
Input-Parameters$sampleCellsRNA: length = 1
[1] 10000
Input-Parameters$embeddingATAC: length = 0
NULL
Input-Parameters$embeddingRNA: length = 0
NULL
Input-Parameters$dimsToUse: length = 30
[1] 1 2 3 4 5 6
Input-Parameters$scaleDims: length = 0
NULL
Input-Parameters$corCutOff: length = 1
[1] 0.75
Input-Parameters$plotUMAP: length = 1
[1] TRUE
Input-Parameters$nGenes: length = 1
[1] 2000
Input-Parameters$useImputation: length = 1
[1] TRUE
Input-Parameters$reduction: length = 1
[1] "cca"
Input-Parameters$addToArrow: length = 1
[1] FALSE
Input-Parameters$scaleTo: length = 1
[1] 10000
Input-Parameters$nameCell: length = 1
[1] "predictedCell_Un"
Input-Parameters$nameGroup: length = 1
[1] "predictedGroup_Un"
Input-Parameters$nameScore: length = 1
[1] "predictedScore_Un"
Input-Parameters$threads: length = 1
[1] 30
Input-Parameters$verbose: length = 1
[1] FALSE
Input-Parameters$force: length = 1
[1] TRUE
Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addGeneIntegrationMatrix-106bc864faf635-Date-2023-09-22_Time-12-24-48.614146.log"
2023-09-22 12:24:49.070918 : Checking ATAC Input, 0.007 mins elapsed.
2023-09-22 12:24:49.080642 : Checking RNA Input, 0.007 mins elapsed.
