eds package for reading in Alevin EDS format

The R package eds provides a single function readEDS for efficiently reading Alevin’s EDS format for single cell count data into R, utilizing the sparse matrix format in the Matrix package.

Note: eds provides a low-level function readEDS which most users will not need to use. Most users and developers will likely prefer to use tximport (for importing matrices) or tximeta (for easy conversion to SingleCellExperiment objects). This package is primarily developed in order to streamline the dependency graph for other packages.

About EDS

EDS is an accronym for Efficient single cell binary Data Storage format for the cell-feature count matrices.

For more details on the EDS format see the following repository:

https://github.com/COMBINE-lab/EDS

Simple example of reading EDS into R:

The following example is the same as round in ?readEDS, first we point to EDS files as output by Alevin:

library(tximportData)
library(eds)
## Loading required package: Matrix
dir0 <- system.file("extdata",package="tximportData")
samps <- list.files(file.path(dir0, "alevin"))
dir <- file.path(dir0,"alevin",samps[3],"alevin")
quant.mat.file <- file.path(dir, "quants_mat.gz")
barcode.file <- file.path(dir, "quants_mat_rows.txt")
gene.file <- file.path(dir, "quants_mat_cols.txt")

readEDS() requires knowing the number of cells and genes, which we find by reading in associated barcode and gene files. Again, note that a more useful convenience function for reading in Alevin data is tximport (matrices) or tximeta (for easy conversion to SingleCellExperiment).

cell.names <- readLines(barcode.file)
gene.names <- readLines(gene.file)
num.cells <- length(cell.names)
num.genes <- length(gene.names)

Finally, reading in the sparse matrix is accomplished with:

mat <- readEDS(
    numOfGenes=num.genes,
    numOfOriginalCells=num.cells,
    countMatFilename=quant.mat.file)

Session info

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] eds_1.0.0           Matrix_1.5-1        tximportData_1.25.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9      lattice_0.20-45 digest_0.6.30   grid_4.2.1     
##  [5] R6_2.5.1        jsonlite_1.8.3  magrittr_2.0.3  evaluate_0.17  
##  [9] stringi_1.7.8   rlang_1.0.6     cachem_1.0.6    cli_3.4.1      
## [13] jquerylib_0.1.4 bslib_0.4.0     rmarkdown_2.17  tools_4.2.1    
## [17] stringr_1.4.1   xfun_0.34       yaml_2.3.6      fastmap_1.1.0  
## [21] compiler_4.2.1  htmltools_0.5.3 knitr_1.40      sass_0.4.2