Gene expression matrix.cvs is too large to load it

I just download human/mouse brain matrix from https://portal.brain-map.org/atlases-and-data/rnaseq and found that these two matrix.csv files were too large to load it by read.csv(filepath,header=T,row.names=1). Is there any advice to load it successfully ? actually, I just want to analyze some cell types, like oligodendrite cells, is there any advice to gain these cells’ expression matrix?

Hi @pommy: I would suggest trying the fread function in the data.table R library. This is typically about 100x faster than read.csv. I don’t know of a way of only loading a subset of the data matrix from a csv file.

Hi @pommy,

We recognize there are some issues loading the full csv. CSVs are not an ideal method for transport, and we intend to have more efficient methods in the near future.

It’s helpful to hear your use case of accessing specific file types.

Here are a few options we’re considering, please feel free to share which of them would work best for your needs:

  • Efficient file format, like hdf5 or LOOM
  • Direct API access
  • Separate downloads by cell type