ReadMtx: Error in url(description = uri) : URL scheme unsupported by this method

[tdoniger]

Using ReadMtx on local files - tried with the whole path to the file or copying them into the current directory-
Always returns:
Error in url(description = uri) : URL scheme unsupported by this method

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=Hebrew_Israel.1255 LC_CTYPE=Hebrew_Israel.1255 LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C
[5] LC_TIME=Hebrew_Israel.1255

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] scater_1.20.1 ggplot2_3.3.5 scuttle_1.2.1 SingleCellExperiment_1.14.1
[5] patchwork_1.1.1 SeuratObject_4.0.4 Seurat_4.0.5 DESeq2_1.32.0
[9] SummarizedExperiment_1.22.0 Biobase_2.52.0 MatrixGenerics_1.4.3 matrixStats_0.61.0
[13] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.2
[17] BiocGenerics_0.38.0 dplyr_1.0.7

loaded via a namespace (and not attached):
[1] plyr_1.8.6 igraph_1.2.7 lazyeval_0.2.2 splines_4.1.1 BiocParallel_1.26.2
[6] listenv_0.8.0 scattermore_0.7 digest_0.6.28 htmltools_0.5.2 viridis_0.6.2
[11] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0 ScaledMatrix_1.0.0 tensor_1.5
[16] cluster_2.1.2 ROCR_1.0-11 globals_0.14.0 Biostrings_2.60.2 annotate_1.70.0
[21] spatstat.sparse_2.0-0 colorspace_2.0-2 blob_1.2.2 ggrepel_0.9.1 crayon_1.4.1
[26] RCurl_1.98-1.5 jsonlite_1.7.2 genefilter_1.74.1 spatstat.data_2.1-0 survival_3.2-13
[31] zoo_1.8-9 glue_1.4.2 polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.38.0
[36] XVector_0.32.0 leiden_0.3.9 DelayedArray_0.18.0 BiocSingular_1.8.1 future.apply_1.8.1
[41] abind_1.4-5 scales_1.1.1 DBI_1.1.1 miniUI_0.1.1.1 Rcpp_1.0.7
[46] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.22 spatstat.core_2.3-2 rsvd_1.0.5
[51] bit_4.0.4 htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2
[56] ica_1.0-2 pkgconfig_2.0.3 XML_3.99-0.8 uwot_0.1.11 deldir_1.0-6
[61] locfit_1.5-9.4 utf8_1.2.2 tidyselect_1.1.1 rlang_0.4.11 reshape2_1.4.4
[66] later_1.3.0 AnnotationDbi_1.54.1 munsell_0.5.0 tools_4.1.1 cachem_1.0.6
[71] generics_0.1.0 RSQLite_2.2.8 ggridges_0.5.3 stringr_1.4.0 fastmap_1.1.0
[76] goftest_1.2-3 bit64_4.0.5 fitdistrplus_1.1-6 purrr_0.3.4 RANN_2.6.1
[81] KEGGREST_1.32.0 pbapply_1.5-0 future_1.23.0 nlme_3.1-153 sparseMatrixStats_1.4.2
[86] mime_0.12 compiler_4.1.1 rstudioapi_0.13 curl_4.3.2 beeswarm_0.4.0
[91] plotly_4.10.0 png_0.1-7 spatstat.utils_2.2-0 tibble_3.1.5 geneplotter_1.70.0
[96] stringi_1.7.5 lattice_0.20-45 Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.4
[101] lifecycle_1.0.1 spatstat.geom_2.3-0 lmtest_0.9-39 BiocNeighbors_1.10.0 RcppAnnoy_0.0.19
[106] data.table_1.14.2 cowplot_1.1.1 bitops_1.0-7 irlba_2.3.3 httpuv_1.6.3
[111] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3 vipor_0.4.5
[116] parallelly_1.28.1 codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 withr_2.4.2
[121] sctransform_0.3.2 GenomeInfoDbData_1.2.6 mgcv_1.8-38 grid_4.1.1 rpart_4.1-15
[126] beachmat_2.8.1 tidyr_1.1.4 DelayedMatrixStats_1.14.3 Rtsne_0.15 shiny_1.7.1
[131] ggbeeswarm_0.6.0

insert reproducible example here

(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4134618)

expression_matrix1 <- ReadMtx( mtx="GSM4134618_CY155_tumor-matrix.mtx.gz", features="GSM4134618_CY155_tumor-genes.tsv.gz", cells="GSM4134618_CY155_tumor-barcodes.tsv.gz")
Error in url(description = uri) : URL scheme unsupported by this method

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. Unfortunately, I can't replicate the error using the same files and copying and pasting your code (though I'm running on Mac OSX and not windows so there may be something specific there). But if you haven't tried it yet I would say try redownloading the files and moving them to project directory and trying again. One of the devs might be able to help with that particular issue if it's Window's specific.

As alternative you could try this function to read in the files:
https://samuel-marsh.github.io/scCustomize/reference/Read10X_GEO.html

Best,
Sam

[saketkc]

Hi @tdoniger, ReadMtx requires the exact path of all the three files to be specific (mtx, features, cells). All GSM4134618_CY155_tumor-*.gz should be in your current director (if not, specify the full path). If you face any issues, please feel free to reopen.