7 Merge data

If cell type classification is performed by experimental units (e.g. batches), the data can be merged into a single Seurat object using the reduce.R script.

Let’s create an output directory to store the results.

mkdir step4_reduce

And check the input arguments

singularity exec -B $PWD cell_classification.sif \  
  Rscript /reduce.R --help

Let’s assume we have a directory called step3_hierscpred containing multiple .RDS files corresponding to different batches. We can merge all Seurat objects follows:

singularity exec -B $PWD cell_classification.sif \ 
            Rscript /reduce.R \
            --file step3_hierscpred \
            --out reduced_data \
            --path step4_reduce

reduce.R will output a single Seurat object called reduced_data.RDS within the step4_reduce directory