A collection of scripts to assess the performance of R & Bioconductor tools working with the 10X Genomics mouse brain data provided in https://github.com/LTLA/TENxBrainData. This is discussed in my blog post at www.msmith.de.
Because some of the tests require installing alternative versions of R packages, which I couldn't achieve reliably once the TENxBrainData package and its dependencies had been loaded, I choose to run each step in a new R session. As a result there is a seperate .Rmd file for each step detailed in the blog post. The names of the files and their purposes are listed below.
| File | Purpose |
|---|---|
| step1.Rmd | Compute column sums using default settings, and compare with in-memory computation |
| step1a.Rmd | Increase the DelayedArray block size |
| step2.Rmd | Create uncompressed dataset and benchmark |
| step3.Rmd | Install and run modified rhdf |
| step3a.Rmd | Install and run modified DelayedArray |
| step4.Rmd | Run with both modified rhdf5 and DelayedArray |
| step5.Rmd | Combine modified package with uncompressed dataset |
| stepN.Rmd | Loads all saved results, checks consistency and produces plots |
Each .Rmd has an initial code block that checks the currently installed versions of rhdf5 and DelayedArray, and installs the version require for the current test if needed. Avoid running them in parallel, partly to reduced the risk of IO competition, but mostly to trying to install two versions of a package simultaneously and corrupting your R library. I have mostly been running the Rmds consecutively in a single batch using the command below:
Rscript -e 'library("rmarkdown"); render("step1.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step1a.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step2.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step3.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step3a.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step4.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("step5.Rmd")' && \
Rscript -e 'library("rmarkdown"); render("stepN.Rmd")'Here is one of the plots produced by stepN.Rmd, detailing the time required to calculate the column sum for each of the first 130,000 columns in TENxBrainData.
