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20 hours ago •
GreenleafLab
GreenleafLab
`addGeneExpressionMatrix` Error: invalid subscript
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Hello
How can I addGeneExpressionMatrix using a SingleCellAssay object?
I created the SingleCellAssay object by:
seRNA <- MAST::FromMatrix(
as.matrix(csr_matrix), #raw counts data, genes in the rows and cells in the columns
cData,
fData,
class = "SingleCellAssay",
check_sanity = FALSE
)
seRNA
Loading required package: MAST
Loading required package: SingleCellExperiment
class: SingleCellAssay
dim: 15515 3157
metadata(0):
assays(1): et
rownames(15515): CreERT2 mKATE_Bglobin ... CAAA01118383.1
CAAA01147332.1
rowData names(10): gene_id function ... std primerid
colnames(3157): TCEV_Multiome1#ATTCAACCATGATTGT-1
TCEV_Multiome1#CAAGGCTGTTGTTCAC-1 ...
TCEV_Multiome3#TTTGTCCCACTTCATC-1 TCEV_Multiome3#TTTGTGAAGTATTGGC-1
colData names(13): cells sample ... umap2 wellKey
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
projHeme3 <- subsetArchRProject(ArchRProj = projHeme2,
cells = colnames(seRNA),
outputDirectory = "ArchRSubset",
dropCells = TRUE,
force = FALSE)
getGenes(projHeme3)
GRanges object with 24368 ranges and 2 metadata columns:
seqnames ranges strand | gene_id symbol
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr1 3214482-3671498 - | 497097 Xkr4
[2] chr1 4290846-4409241 - | 19888 Rp1
[3] chr1 4490928-4497354 - | 20671 Sox17
[4] chr1 4773198-4785726 - | 27395 Mrpl15
[5] chr1 4807893-4846735 + | 18777 Lypla1
... ... ... ... . ... ...
[24364] chrY 66739797-66742170 - | 100040786 Gm20852
[24365] chrY 78835721-78836719 - | 100039574 Gm20806
[24366] chrY 79148793-79149787 - | 100042428 Gm20917
[24367] chrY 85528523-85529519 - | 100040911 Gm20854
[24368] chrY 90784610-90816465 + | 170942 Erdr1
-------
seqinfo: 21 sequences from mm10 genome
rowData(seRNA)[1:5]
DataFrame with 15515 rows and 5 columns
symbol function n_cells highly_variable
<character> <factor> <integer> <logical>
CreERT2 CreERT2 Gene Expression 85 FALSE
mKATE_Bglobin mKATE_Bglobin Gene Expression 1898 FALSE
MYC_SV40pA MYC_SV40pA Gene Expression 1117 TRUE
Xkr4 Xkr4 Gene Expression 38 FALSE
Rp1 Rp1 Gene Expression 32 FALSE
... ... ... ... ...
Vamp7 Vamp7 Gene Expression 158 FALSE
Tmlhe Tmlhe Gene Expression 238 FALSE
AC149090.1 AC149090.1 Gene Expression 785 FALSE
CAAA01118383.1 CAAA01118383.1 Gene Expression 791 FALSE
CAAA01147332.1 CAAA01147332.1 Gene Expression 34 FALSE
means
<numeric>
CreERT2 0.0532844
mKATE_Bglobin 1.4895195
MYC_SV40pA 0.9191971
Xkr4 0.0237930
Rp1 0.0211868
... ...
Vamp7 0.0806509
Tmlhe 0.1489885
AC149090.1 0.4397101
CAAA01118383.1 0.4414484
CAAA01147332.1 0.0184182
proj <- addGeneExpressionMatrix(input = projHeme3,
seRNA = seRNA,
force = TRUE,
strictMatch = TRUE)
ArchR logging to : ArchRLogs/ArchR-addGeneExpressionMatrix-3bc58765440-Date-2024-10-17_Time-09-55-16.395514.log
If there is an issue, please report to github with logFile!
Overlap w/ scATAC = 1
2024-10-17 09:55:17.974571 :
Overlap Per Sample w/ scATAC : TCEV_Multiome1=687,TCEV_Multiome2=669,TCEV_Multiome3=1801
2024-10-17 09:55:17.990951 :
NULL
Error: invalid subscript
Traceback:
1. seRNA[BiocGenerics::which(seqnames(seRNA) %bcin% seqnames(chromSizes))]
2. seRNA[BiocGenerics::which(seqnames(seRNA) %bcin% seqnames(chromSizes))]
3. int_elementMetadata(x)[ii, , drop = FALSE]
4. int_elementMetadata(x)[ii, , drop = FALSE]
5. extractROWS(x, i)
6. extractROWS(x, i)
7. normalizeSingleBracketSubscript(i, x, allow.NAs = TRUE, as.NSBS = TRUE)
8. NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
. allow.NAs = allow.NAs)
9. NSBS(i, x, exact = exact, strict.upper.bound = !allow.append,
. allow.NAs = allow.NAs)
10. .subscript_error("invalid subscript")
11. stop(wmsg(...), call. = FALSE)
12. .handleSimpleError(function (cnd)
. {
. watcher$capture_plot_and_output()
. cnd <- sanitize_call(cnd)
. watcher$push(cnd)
. switch(on_error, continue = invokeRestart("eval_continue"),
. stop = invokeRestart("eval_stop"), error = invokeRestart("eval_error",
. cnd))
. }, "invalid subscript", base::quote(NULL))
The ArchRLogs/ArchR-addGeneExpressionMatrix-3bc58765440-Date-2024-10-17_Time-09-55-16.395514.log:
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
Logging With ArchR!
Start Time : 2024-10-17 09:55:16.436662
------- ArchR Info
ArchRThreads = 10
ArchRGenome = Mm10
------- System Info
Computer OS = unix
Total Cores = 12
------- Session Info
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 grid stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] SeuratObject_4.1.3 Seurat_4.3.0
[3] MAST_1.30.0 SingleCellExperiment_1.26.0
[5] rhdf5_2.48.0 SummarizedExperiment_1.34.0
[7] Biobase_2.64.0 MatrixGenerics_1.16.0
[9] Rcpp_1.0.13 Matrix_1.7-0
[11] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[13] IRanges_2.38.1 S4Vectors_0.42.1
[15] BiocGenerics_0.50.0 matrixStats_1.4.1
[17] data.table_1.16.0 stringr_1.5.1
[19] plyr_1.8.9 magrittr_2.0.3
[21] ggplot2_3.5.1 gtable_0.3.5
[23] gtools_3.9.5 gridExtra_2.3
[25] ArchR_1.0.2
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.1
[3] later_1.3.2 pbdZMQ_0.3-11
[5] BiocIO_1.14.0 bitops_1.0-8
[7] tibble_3.2.1 polyclip_1.10-7
[9] XML_3.99-0.17 lifecycle_1.0.4
[11] globals_0.16.3 lattice_0.22-6
[13] MASS_7.3-61 plotly_4.10.4
[15] yaml_2.3.10 httpuv_1.6.15
[17] sctransform_0.4.1 sp_2.1-4
[19] spatstat.sparse_3.1-0 reticulate_1.38.0
[21] cowplot_1.1.3 pbapply_1.7-2
[23] RColorBrewer_1.1-3 abind_1.4-8
[25] zlibbioc_1.50.0 Rtsne_0.17
[27] purrr_1.0.2 RCurl_1.98-1.16
[29] GenomeInfoDbData_1.2.12 ggrepel_0.9.6
[31] irlba_2.3.5.1 listenv_0.9.1
[33] spatstat.utils_3.0-5 goftest_1.2-3
[35] spatstat.random_3.3-1 fitdistrplus_1.2-1
[37] parallelly_1.38.0 leiden_0.4.3.1
[39] codetools_0.2-20 DelayedArray_0.30.1
[41] tidyselect_1.2.1 UCSC.utils_1.0.0
[43] base64enc_0.1-3 spatstat.explore_3.3-1
[45] GenomicAlignments_1.40.0 jsonlite_1.8.9
[47] progressr_0.14.0 ggridges_0.5.6
[49] survival_3.7-0 tools_4.4.1
[51] ica_1.0-3 glue_1.7.0
[53] SparseArray_1.4.8 IRdisplay_1.1
[55] dplyr_1.1.4 withr_3.0.1
[57] fastmap_1.2.0 rhdf5filters_1.16.0
[59] fansi_1.0.6 digest_0.6.37
[61] R6_2.5.1 mime_0.12
[63] colorspace_2.1-1 scattermore_1.2
[65] tensor_1.5 spatstat.data_3.1-2
[67] utf8_1.2.4 tidyr_1.3.1
[69] generics_0.1.3 rtracklayer_1.64.0
[71] httr_1.4.7 htmlwidgets_1.6.4
[73] S4Arrays_1.4.1 uwot_0.2.2
[75] pkgconfig_2.0.3 lmtest_0.9-40
[77] XVector_0.44.0 htmltools_0.5.8.1
[79] scales_1.3.0 png_0.1-8
[81] spatstat.univar_3.0-0 reshape2_1.4.4
[83] rjson_0.2.23 uuid_1.2-1
[85] nlme_3.1-166 curl_5.2.3
[87] repr_1.1.7 zoo_1.8-12
[89] KernSmooth_2.23-24 miniUI_0.1.1.1
[91] restfulr_0.0.15 pillar_1.9.0
[93] vctrs_0.6.5 RANN_2.6.1
[95] promises_1.3.0 xtable_1.8-4
[97] cluster_2.1.6 evaluate_1.0.0
[99] cli_3.6.3 compiler_4.4.1
[101] Rsamtools_2.20.0 rlang_1.1.4
[103] crayon_1.5.3 future.apply_1.11.2
[105] stringi_1.8.4 viridisLite_0.4.2
[107] deldir_2.0-4 BiocParallel_1.38.0
[109] munsell_0.5.1 Biostrings_2.72.1
[111] lazyeval_0.2.2 spatstat.geom_3.3-2
[113] IRkernel_1.3.2 BSgenome_1.72.0
[115] patchwork_1.2.0 future_1.34.0
[117] Rhdf5lib_1.26.0 shiny_1.9.1
[119] ROCR_1.0-11 igraph_2.0.3
[121] BSgenome.Mmusculus.UCSC.mm10_1.4.3
------- Log Info
2024-10-17 09:55:16.571968 : addGeneExpressionMatrix Input-Parameters, Class = list
addGeneExpressionMatrix Input-Parameters$input: length = 1
addGeneExpressionMatrix Input-Parameters$seRNA: length = 15515
class: SingleCellAssay
dim: 6 3157
metadata(0):
assays(1): et
rownames(6): CreERT2 mKATE_Bglobin ... Rp1 Sox17
rowData names(10): gene_id function ... std primerid
colnames(3157): TCEV_Multiome1#ATTCAACCATGATTGT-1
TCEV_Multiome1#CAAGGCTGTTGTTCAC-1 ...
TCEV_Multiome3#TTTGTCCCACTTCATC-1 TCEV_Multiome3#TTTGTGAAGTATTGGC-1
colData names(13): cells sample ... umap2 wellKey
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
addGeneExpressionMatrix Input-Parameters$chromSizes: length = 21
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 1-195471971 *
[2] chr2 1-182113224 *
[3] chr3 1-160039680 *
[4] chr4 1-156508116 *
[5] chr5 1-151834684 *
[6] chr6 1-149736546 *
-------
seqinfo: 21 sequences from an unspecified genome
addGeneExpressionMatrix Input-Parameters$excludeChr: length = 2
[1] "chrM" "chrY"
addGeneExpressionMatrix Input-Parameters$scaleTo: length = 1
[1] 10000
addGeneExpressionMatrix Input-Parameters$verbose: length = 1
[1] TRUE
addGeneExpressionMatrix Input-Parameters$threads: length = 1
[1] 10
addGeneExpressionMatrix Input-Parameters$parallelParam: length = 0
NULL
addGeneExpressionMatrix Input-Parameters$strictMatch: length = 1
[1] TRUE
addGeneExpressionMatrix Input-Parameters$force: length = 1
[1] TRUE
addGeneExpressionMatrix Input-Parameters$logFile: length = 1
[1] "ArchRLogs/ArchR-addGeneExpressionMatrix-3bc58765440-Date-2024-10-17_Time-09-55-16.395514.log"
2024-10-17 09:55:17.976565 :
2024-10-17 09:55:17.992817 :
Hi @danli349! 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.
