Read10X in PBMC3K tutorial

[kvijayendran]

I am going through the PBMC3K tutorial. I downloaded the latest version of Seurat (version 4.0), R studio (1.4.1103), and R version 4.0.3. The following code is throwing an error:

pbmc.data <- Read10X(data.dir = "../filtered_gene_bc_matrices/hg19/")

This is the error:
Error in Read10X(data.dir = "../filtered_gene_bc_matrices/hg19/") :
could not find function "Read10X"

My colleague is using the previous version of Seurat, and this line of code is running fine. Is there a problem with the Read10X function in the latest version of Seurat?

Thanks for your help.

[timoast]

Can you post the output of sessionInfo()?

[kvijayendran]

Hi Timoast,

Output is below. Also: I installed the dpylr, Seurat and patchwork packages. But when I run library(Seurat), it gives this output:

Error: package or namespace load failed for ‘Seurat’:
object ‘wrap_plots’ is not exported by 'namespace:patchwork'

Here is the sessionInfo() output:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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
[7] base

other attached packages:
[1] patchwork_2.4 dplyr_1.0.4

loaded via a namespace (and not attached):
[1] SeuratObject_4.0.0 ggrepel_0.9.1 Rcpp_1.0.6
[4] lattice_0.20-41 ica_1.0-2 listenv_0.8.0
[7] zoo_1.8-9 lmtest_0.9-38 assertthat_0.2.1
[10] digest_0.6.27 mime_0.9 parallelly_1.23.0
[13] R6_2.5.0 plyr_1.8.6 ggridges_0.5.3
[16] httr_1.4.2 ggplot2_3.3.3 pillar_1.4.7
[19] rlang_0.4.10 miniUI_0.1.1.1 irlba_2.3.3
[22] leiden_0.3.7 Matrix_1.3-2 reticulate_1.18
[25] splines_4.0.3 Rtsne_0.15 stringr_1.4.0
[28] igraph_1.2.6 munsell_0.5.0 tinytex_0.29
[31] shiny_1.6.0 sctransform_0.3.2 httpuv_1.5.5
[34] compiler_4.0.3 xfun_0.20 pkgconfig_2.0.3
[37] htmltools_0.5.1.1 globals_0.14.0 tidyselect_1.1.0
[40] tibble_3.0.6 gridExtra_2.3 RANN_2.6.1
[43] codetools_0.2-18 matrixStats_0.58.0 fitdistrplus_1.1-3
[46] future_1.21.0 later_1.1.0.1 crayon_1.4.0
[49] MASS_7.3-53 grid_4.0.3 xtable_1.8-6
[52] jsonlite_1.7.2 gtable_0.3.0 lifecycle_0.2.0
[55] DBI_1.1.1 magrittr_2.0.1 scales_1.1.1
[58] KernSmooth_2.23-18 future.apply_1.7.0 stringi_1.5.3
[61] ROCR_1.0-11 reshape2_1.4.4 promises_1.1.1
[64] ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6
[67] cowplot_1.1.1 RcppAnnoy_0.0.18 RColorBrewer_1.1-2
[70] tools_4.0.3 glue_1.4.2 purrr_0.3.4
[73] fastmap_1.1.0 parallel_4.0.3 survival_3.2-7
[76] colorspace_2.0-0 cluster_2.1.0

[timoast]

Since you got an error when loading the Seurat package, the library is not loaded as so you can't use functions from the package. This is why you have an error "cannot find function Read10X". I'd suggest reinstalling patchwork, and if that doesn't solve the issue try reinstalling Seurat