Last updated: 2025-06-05
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Knit directory: muse/
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Ignored: .Rproj.user/
Ignored: data/1M_neurons_filtered_gene_bc_matrices_h5.h5
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Ignored: data/293t_3t3_filtered_gene_bc_matrices.tar.gz
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Ignored: data/pbmc3k/
Ignored: data/pbmc3k_bpcells_mat/
Ignored: data/pbmc3k_export.mtx
Ignored: data/pbmc3k_matrix.mtx
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | cc627f7 | Dave Tang | 2025-06-05 | CsparseMatrix |
| html | e6f872a | Dave Tang | 2025-06-05 | Build site. |
| Rmd | e53b097 | Dave Tang | 2025-06-05 | Matrix Market format |
Matrix Market exchange formats:
The Matrix Market exchange formats are a set of human readable, ASCII-based file formats designed to facilitate the exchange of matrix data. The file formats were designed and adopted for the Matrix Market, a NIST repository for test data for use in comparative studies of algorithms for numerical linear algebra.
Download Matrix Market file.
my_url <- 'https://davetang.org/file/pbmc3k/filtered_gene_bc_matrices/hg19/matrix.mtx'
mtx_file <- "data/pbmc3k_matrix.mtx"
if(!file.exists(mtx_file)){
download.file(url = my_url, destfile = mtx_file)
}The {Matrix} package has support for Matrix Market using
readMM() and writeMM().
my_mat <- Matrix::readMM(mtx_file)
class(my_mat)[1] "dgTMatrix"
attr(,"package")
[1] "Matrix"Convert dgTMatrix to dgCMatrix.
| Feature | dgCMatrix |
dgTMatrix |
|---|---|---|
| Name | Double General Compressed Column | Double General Triplet |
| Format | CSC (Compressed Sparse Column) | COO (Coordinate / Triplet) |
| Storage | Uses column pointers + row indices | Stores each non-zero entry’s (row, col, val) |
| Construction | Less intuitive (needs compressed structure) | Easy to build from scratch |
| Efficiency | Fast and memory-efficient | Slower and less compact |
dgCMatrix is a CsparseMatrix.
my_mat <- as(my_mat, "CsparseMatrix")
class(my_mat)[1] "dgCMatrix"
attr(,"package")
[1] "Matrix"Export.
Matrix::writeMM(obj = my_mat, file = "data/pbmc3k_export.mtx")NULL
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 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/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[9] ggplot2_3.5.2 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.10 generics_0.1.4 lattice_0.22-6 stringi_1.8.7
[5] hms_1.1.3 digest_0.6.37 magrittr_2.0.3 timechange_0.3.0
[9] evaluate_1.0.3 grid_4.5.0 RColorBrewer_1.1-3 fastmap_1.2.0
[13] Matrix_1.7-3 rprojroot_2.0.4 jsonlite_2.0.0 processx_3.8.6
[17] whisker_0.4.1 ps_1.9.1 promises_1.3.2 httr_1.4.7
[21] scales_1.4.0 jquerylib_0.1.4 cli_3.6.5 rlang_1.1.6
[25] withr_3.0.2 cachem_1.1.0 yaml_2.3.10 tools_4.5.0
[29] tzdb_0.5.0 httpuv_1.6.16 vctrs_0.6.5 R6_2.6.1
[33] lifecycle_1.0.4 git2r_0.36.2 fs_1.6.6 pkgconfig_2.0.3
[37] callr_3.7.6 pillar_1.10.2 bslib_0.9.0 later_1.4.2
[41] gtable_0.3.6 glue_1.8.0 Rcpp_1.0.14 xfun_0.52
[45] tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.50 farver_2.1.2
[49] htmltools_0.5.8.1 rmarkdown_2.29 compiler_4.5.0 getPass_0.2-4