Overview

magicBatch is a modified version of the MAGIC algorithm that allows for batch-corrected imputation of multi-batch datasets.

Installation

  1. install the magicBatch python package using one of two methods:

    From within R (preferred):

    python_path <- system("which python3", intern = TRUE)
system(paste(python_path, "-m pip install magicBatch"))

    From the command line:

    pip install magicBatch

    And copy the output of

    which python

    as this will be needed to invoke the correct python runtime from within R.

  2. install the magicBatch R package:

    devtools::install_github("kbrulois/magicBatch")

Usage 

library(magicBatch)

python_path <- system("which python3", intern = TRUE) 
#python_path <- "path/to/venv/bin/python"
#python_path <- "/path/to/python3.x"

sce <- readRDS(url('https://stacks.stanford.edu/file/druid:cf352cg6610/PLN123_SCE.rds'))

MAGIC_w_correction <- magicBatch(data = as.matrix(t(logcounts(sce))), 
                                 mar_mat_input = reducedDim(sce, "MNN_correction"),
                                 t_param = 6, 
                                 python_command = python_path)

Tutorial

Please see package website for full documentation:

https://kbrulois.github.io/magicBatch/articles/batch_correction.html