Not able to convert loom to seurat
millerkaplanlab opened this issue · 6 comments
millerkaplanlab commented
Hello. I used velocyto to generate the loom file required to RNA Velocity using seurat wrappers. I am unable to convert the loom object to Seurat as shown in the tutorial. I get the following error. Any help would be appreciated.
P7loom <- as.Seurat(x = loom.data)
| | 0%Error in validObject(.Object) :
invalid class “LogMap” object: Duplicate rownames not allowed
FlyingFa commented
Similar problem, did you figure out ?
jcy258 commented
Same problem!
jwtobias commented
Please add me to the list. Same function, same error.
TaoBern commented
same as me , does anyone solve it?
hwick commented
I am having the same issue
> ldat <- ReadVelocity(file = "../velocyto_out/merged_loom/all_merged.loom")
reading loom file via hdf5r...
> # Turn loom to seurat
> bm <- as.Seurat(x = ldat)
| | 0%Error in validObject(.Object) :
invalid class “LogMap” object: Duplicate rownames not allowed
> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.3.19-gcc-9.2.0/lib/libopenblas_haswellp-r0.3.19.so; LAPACK version 3.9.0
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: US/Eastern
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] loomR_0.2.0 itertools_0.1-3 iterators_1.0.14 hdf5r_1.3.11
[5] R6_2.5.1 SeuratWrappers_0.3.5 SeuratDisk_0.0.0.9021 Seurat_5.1.0
[9] SeuratObject_5.0.2 sp_2.1-4 pcaMethods_1.96.0 Biobase_2.64.0
[13] BiocGenerics_0.50.0 devtools_2.4.5 usethis_3.0.0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3
[5] spatstat.utils_3.0-5 fs_1.6.4 vctrs_0.6.5 ROCR_1.0-11
[9] memoise_2.0.1 spatstat.explore_3.3-1 htmltools_0.5.8.1 curl_5.2.1
[13] sctransform_0.4.1 parallelly_1.38.0 KernSmooth_2.23-22 htmlwidgets_1.6.4
[17] desc_1.4.3 ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[21] zoo_1.8-12 cachem_1.1.0 igraph_2.0.3 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 rsvd_1.0.5 Matrix_1.7-0
[29] fastmap_1.2.0 fitdistrplus_1.2-1 future_1.34.0 shiny_1.9.1
[33] digest_0.6.36 colorspace_2.1-1 patchwork_1.2.0 ps_1.7.7
[37] tensor_1.5 RSpectra_0.16-2 irlba_2.3.5.1 pkgload_1.4.0
[41] progressr_0.14.0 fansi_1.0.6 spatstat.sparse_3.1-0 mgcv_1.9-1
[45] httr_1.4.7 polyclip_1.10-7 abind_1.4-5 compiler_4.4.0
[49] remotes_2.5.0 withr_3.0.1 bit64_4.0.5 fastDummies_1.7.3
[53] pkgbuild_1.4.4 R.utils_2.12.3 MASS_7.3-60.2 sessioninfo_1.2.2
[57] tools_4.4.0 lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.2
[61] goftest_1.2-3 R.oo_1.26.0 glue_1.7.0 callr_3.7.6
[65] nlme_3.1-164 promises_1.3.0 grid_4.4.0 Rtsne_0.17
[69] cluster_2.1.6 reshape2_1.4.4 generics_0.1.3 gtable_0.3.5
[73] spatstat.data_3.1-2 R.methodsS3_1.8.2 tidyr_1.3.1 data.table_1.15.4
[77] utf8_1.2.4 spatstat.geom_3.3-2 RcppAnnoy_0.0.22 ggrepel_0.9.5
[81] RANN_2.6.1 pillar_1.9.0 stringr_1.5.1 spam_2.10-0
[85] RcppHNSW_0.6.0 later_1.3.2 splines_4.4.0 dplyr_1.1.4
[89] lattice_0.22-6 bit_4.0.5 survival_3.5-8 deldir_2.0-4
[93] tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[97] scattermore_1.2 matrixStats_1.3.0 stringi_1.8.4 lazyeval_0.2.2
[101] codetools_0.2-20 tibble_3.2.1 BiocManager_1.30.23 cli_3.6.3
[105] uwot_0.2.2 xtable_1.8-4 reticulate_1.38.0 munsell_0.5.1
[109] processx_3.8.4 Rcpp_1.0.13 globals_0.16.3 spatstat.random_3.3-1
[113] png_0.1-8 spatstat.univar_3.0-0 parallel_4.4.0 ellipsis_0.3.2
[117] ggplot2_3.5.1 velocyto.R_0.6 dotCall64_1.1-1 profvis_0.3.8
[121] urlchecker_1.0.1 listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[125] ggridges_0.5.6 crayon_1.5.3 leiden_0.4.3.1 purrr_1.0.2
[129] rlang_1.1.4 cowplot_1.1.3