I have an hdf5 file that I would like to read the subgroup of it.
the file 'GSE77565_FBD_IC-heatmap-chr-10k.hdf5.gz' is downloaded from GEO number= 'GSE77565'
I read the data like below:
library(rhdf5) h5f = H5Fopen("file.hdf5") h5f HDF5 FILE name / filename name otype dclass dim 0 (0, 0) H5I_DATASET FLOAT 24926 x 24926 1 (1, 1) H5I_DATASET FLOAT 24320 x 24320 2 (10, 10) H5I_DATASET FLOAT 13501 x 13501
but when I want to read one of the name I faced wth error:
h5f$"(1, 1)" Error: Unable to read dataset. Not all required filters available. Missing filters: lzf
Also, I could not open any subgroup:
h5f_1 = H5Fopen("file.hdf5","(1, 1)") Error: Unable to read dataset. Not all required filters available. Missing filters: lzf In addition: Warning message: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. h5f&"(1, 1)" HDF5 DATASET name /(1, 1) filename type H5T_IEEE_F64LE rank 2 size 24320 x 24320 maxsize 24320 x 24320