The 10X.R script is meant to 

Lines 4-6 should be uncommented and run ONLY if the "cellrangerRkit" package has not already installed from CRAN.

The directory structure generated by the 10X Cell Ranger software needs to be replicated in the local directory.
Specifically, the pwd should be set to the parent folder for the matrix file first. **Note this has to be the parent directory for the "outs" folder.
##**Note** directory structure MUST be: "/sample_name/outs/filtered_gene_bc_matrices/outs", with the last "outs" containing the barcodes.tsv, genes.tsv, and matrix.mtx files.

The script should be run for each of the 10X Cell Ranger files generated. Ensure that the output file name (in line 39) is changed appropriately prior to each time the script is run.