genecell / cosgr Goto Github PK

Hi!

I'm trying to run your usage sample and I am having an error when running this part:

####### Run COSG for selected groups, i.e., '0' and 2':
#######
marker_cosg <- cosg(
 pbmc_small,
 groups=c('0', '2'),
 assay='RNA',
 slot='data',
 mu=1,
 n_genes_user=100)

I get the error:

Error in if (groups == "all") { : the condition has length > 1

Apparently, because the object groups has more than 1 condition, it triggers an if statement error. How do you overcome this?

Thank you!

Thank you very much for this package, it will greatly reduce the time for us to select unique gene.

But I found that there are only tutorials used in Seurat and Scanpy on github. How can it be used in scATAC and spatial?

For example, how can it be integrated into the ArchR workflow? thank you very much.

Is there any way to solve the problem?

marker_cosg <- cosg(scRNA_object, groups='all',assay='SCT',

•                 slot='data',mu=1,n_genes_user=100,
  

•                 remove_lowly_expressed=TRUE,
  

•                 expressed_pct=0.1)
  

Error in ..subscript.2ary(x, l[[1L]], l[[2L]], drop = drop[1L]) :
NA subscripts in x[i,j] not supported for 'x' inheriting from sparseMatrix
addition: Warning message:
x or y has vectors with all zero; consider setting use_nan = TRUE to set these values to NaN or use_nan = FALSE to suppress this warning

Hi,

Thank you for sharing the wonderful method. Recently, I ran into issues with my new Apple silicon computer when I use cosg with a Seurat object. I could not figure out what was the problem. I will appreciate it if you can help.

marker_cosg <- COSG::cosg(seu, groups='all', assay='RNA', slot='data', mu=1, n_genes_user=2) \

Error in tabulate(genexcell[, idx_i]@i + 1) :
trying to get slot "i" from an object of a basic class ("matrix") with no slots

Here is my sessionInfo:

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] forcats_0.5.2 stringr_1.5.0 dplyr_1.0.10 purrr_1.0.1 readr_2.1.3
[6] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.4.0 tidyverse_1.3.2 SeuratObject_4.1.3
[11] Seurat_4.3.0

loaded via a namespace (and not attached):
[1] googledrive_2.0.0 Rtsne_0.16 colorspace_2.0-3 deldir_1.0-6
[5] ellipsis_0.3.2 ggridges_0.5.4 fs_1.5.2 rstudioapi_0.14
[9] spatstat.data_3.0-0 leiden_0.4.3 listenv_0.9.0 ggrepel_0.9.2
[13] lubridate_1.9.0 fansi_1.0.3 xml2_1.3.3 codetools_0.2-18
[17] splines_4.2.2 polyclip_1.10-4 jsonlite_1.8.4 COSG_0.9.0
[21] broom_1.0.2 ica_1.0-3 cluster_2.1.4 dbplyr_2.3.0
[25] png_0.1-8 uwot_0.1.14 shiny_1.7.4 sctransform_0.3.5
[29] spatstat.sparse_3.0-0 compiler_4.2.2 httr_1.4.4 backports_1.4.1
[33] assertthat_0.2.1 Matrix_1.5-3 fastmap_1.1.0 lazyeval_0.2.2
[37] gargle_1.2.1 cli_3.6.0 later_1.3.0 htmltools_0.5.4
[41] tools_4.2.2 igraph_1.3.5 gtable_0.3.1 glue_1.6.2
[45] RANN_2.6.1 reshape2_1.4.4 Rcpp_1.0.9 scattermore_0.8
[49] cellranger_1.1.0 vctrs_0.5.1 spatstat.explore_3.0-5 nlme_3.1-160
[53] progressr_0.13.0 lmtest_0.9-40 spatstat.random_3.0-1 globals_0.16.2
[57] rvest_1.0.3 timechange_0.2.0 mime_0.12 miniUI_0.1.1.1
[61] lifecycle_1.0.3 irlba_2.3.5.1 googlesheets4_1.0.1 goftest_1.2-3
[65] future_1.30.0 MASS_7.3-58.1 zoo_1.8-11 scales_1.2.1
[69] hms_1.1.2 promises_1.2.0.1 spatstat.utils_3.0-1 parallel_4.2.2
[73] RColorBrewer_1.1-3 reticulate_1.27 pbapply_1.7-0 gridExtra_2.3
[77] stringi_1.7.12 rlang_1.0.6 pkgconfig_2.0.3 matrixStats_0.63.0
[81] lattice_0.20-45 ROCR_1.0-11 tensor_1.5 patchwork_1.1.2
[85] htmlwidgets_1.6.1 cowplot_1.1.1 tidyselect_1.2.0 parallelly_1.34.0
[89] RcppAnnoy_0.0.20 plyr_1.8.8 magrittr_2.0.3 R6_2.5.1
[93] generics_0.1.3 DBI_1.1.3 withr_2.5.0 haven_2.5.1
[97] pillar_1.8.1 proxyC_0.3.3 fitdistrplus_1.1-8 survival_3.4-0
[101] abind_1.4-5 sp_1.5-1 future.apply_1.10.0 crayon_1.5.2
[105] modelr_0.1.10 KernSmooth_2.23-20 utf8_1.2.2 spatstat.geom_3.0-3
[109] plotly_4.10.1 tzdb_0.3.0 readxl_1.4.1 grid_4.2.2
[113] data.table_1.14.6 reprex_2.0.2 digest_0.6.31 xtable_1.8-4
[117] httpuv_1.6.8 RcppParallel_5.1.6 munsell_0.5.0 viridisLite_0.4.1

Hi

thanks for the great tool. I just noticed that I can't use the groups options to run on specific identities due to the fact that in Seurat V4 subset is not in Seurat but in the SeuratObject library.

cheers
daniel