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An R interface to the subsampling algorithms implemented in python
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fmicompbio/sketchR
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sketchR provides a simple interface to thegeosketch andscSamplerpython packages, which implement subsampling algorithms described inHie et al (2019)andSong et al (2022),respectively. The implementation makes use of thebasiliskpackage for interaction between R and python.
You can installsketchR from Bioconductor (release 3.19 onwards) using:
if (!require("BiocManager",quietly=TRUE)) install.packages("BiocManager")BiocManager::install("sketchR")
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)
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An R interface to the subsampling algorithms implemented in python
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