hc-28 loading dataset in R

Grad student in Jadhav Lab here.

We formatted the code and dataset for Matlab. But I do have some suggestions that you can try to munge/shape this data into R.

Looking at your output, it's as if every nested list in spikes{day}{epoch}{tetrode}{cell}--4 total layers of nested list in Matlab--are each being read in as 2 levels of list instead of 1. This is because each cell/list in matlab's memory are stored as spikes{1,day}{1,epoch}{1,tetrode}{1,cell}. A matrix at each level.

When you call matlab.R::readMat(), it is not squeezing this 2-dimensional cell structure at each level/list. It's reading each list level as if it were a matrix (2 indices) instead of a vector (1 index). This doubles the required indices into the data. So for R, to index into day 1, epoch 4, tetrode 27, cell 2, you simply write:

spikes[[1]][[1]][[1]][[4]][[1]][[27]][[1]][[2]]

Second, if that doesn't work, you can also try Python. We have used scipy.io.loadmat() or hdfstorage.io.loadmat functions to read in the data, with the squeeze_me=true option. This eliminates the index doubling above. And then you can save those leaner variables with numpy.savez and use R's package for the .npz format.

Lastly, a quick shout-out to some other useful resources: The hc-6, hc-13, and hc-26 share our dataset format. And hc-26 links to a rep with some basic preprocessing and analysis code you can use on this dataset.