Closed luozhy88 closed 1 year ago
The attributes of hdf5 doesn't allow to store colnames of very large size.
The idea is that the Genename 'Gene0001' is converted to 1, etc. This allows to have a pure matrix of numbers.
What I suggest is to parse your gene annotations e.g. eggnog and transform the 'Gene0001' is converted to 1. I don't know on top of my head how to do this in R but I can try to find a way.
Note: on the master branch I have the option to annotate genecatalog with kegg via dram .
Just to be shure the code snipped you send worked, isn't it?
Thank you for your advice. It worked.
Thank you very much for developing such a useful tool. I have a problem that needs help.The median_coverage.h5 is no rowname(gene name)
filename = "counts/median_coverage.h5" data <- h5read(filename, "data") attributes= h5readAttributes(filename, "data") colnames(data) <- attributes$sample_names