Reading .h5 file in R

Question

I have a '.h5' file and want to extract it using R.

I searched and found rhdf5 from BiocManager is used for this purpose. I tried it and I got an error. No matter if I use either 'h5ls' or 'h5read' methods, I always get the same error message below.

Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file.

file_url <- "data/MillionSongSubset/AdditionalFiles/subset_msd_summary_file.h5"
h5ls(file_url)
data <- h5read(file_url)

I want to extract my '.h5' file either csv or another type in order to use them in R.

Answer 1

This is a Windows problem. I had it commonly either trying to open .tsv or .h5 processed by Kallisto (using, in my case, txtimport). Move you file of folder away from "my documents", e.g. to c:[YOURFOLDER]. That should solve your problem.