Bioconductor Code: sketchR (original) (raw)

# sketchR
[\](https://github.com/fmicompbio/sketchR/actions) `sketchR` provides a simple interface to the [`geosketch`](https://github.com/brianhie/geosketch) and [`scSampler`](https://github.com/SONGDONGYUAN1994/scsampler) python packages, which implement subsampling algorithms described in [Hie et al (2019)](https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30152-8) and [Song et al (2022)](https://www.biorxiv.org/content/10.1101/2022.01.15.476407v1), respectively. The implementation makes use of the [`basilisk`](https://bioconductor.org/packages/basilisk/) package for interaction between R and python. ## Installation You can install `sketchR` from Bioconductor (release 3.19 onwards) using: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("sketchR") ``` ## Example ``` r library(sketchR) ## Create an example data matrix. Rows represent "samples" (the unit of ## downsampling), columns represent features (e.g., principal components). mat <- matrix(rnorm(5000), nrow = 500) ## Run geosketch. The output is a vector of indices, which you can use ## to subset the rows of the input matrix. idx <- geosketch(mat, N = 100) ## Run scSampler. As for geosketch, the output is a vector of indices. idx2 <- scsampler(mat, N = 100) ```