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joey711 / biom

Development version of the biom package for R
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BIOM format 1.0.0 json file load_biom error #20

Closed chrishah closed 8 years ago

chrishah commented 8 years ago

Hi, I am looking to load a biom file that I have produced with the biom-format python package (version 2.1.4) into R. It's definitely in json format - it was produced using the biom-format function Table.to_json().

I am using R biom package version 0.3.12. When I do:

biom.test <- read_biom('test-OTU-taxonomy.kraken.biom')

I get:

Error in if (!object$type %in% biomtypevals) { : 
  argument is of length zero

The file loads fine into phinch. Any advice on how I could get this to work would be massively appreciated!

I attach the actual biom table (just added .txt so Github would accept the upload) - Thanks in advance for you help!

test-OTU-taxonomy.kraken.biom.txt

cheers, Christoph

joey711 commented 8 years ago

"biom" on CRAN should be considered deprecated and is going to disappear soon. Its improvements, including support for HDF5, are included in the biomformat package on Bioconductor.

If you still have this problem after trying that package, re-post this issue on the biomformat repo issue tracker.

Thanks!