Hello- I am trying to convert an available loom file to Seurat. The convert documentation seems to support conversion to/from loom but I am having difficulty getting it to work. Any help would be greatly appreciated!
hdf5r is updated (hdf5r_1.0.1); loomR is updated (loomR_0.2.0). (see below for complex session info)
Here is the command followed by the error:
S_object <- Convert(from= lfile, to= "seurat") `Error in UseMethod(generic = "Convert", object = from) : no applicable method for 'Convert' applied to an object of class "c('loom', 'H5File', 'H5RefClass', 'R6')" sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.2 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  splines stats4 parallel stats graphics grDevices utils  datasets methods base other attached packages:  loomR_0.2.0 itertools_0.1-3 iterators_1.0.10  hdf5r_1.0.1 R6_2.3.0 monocle_2.10.0  DDRTree_0.1.5 irlba_2.3.2 VGAM_1.0-6  Biobase_2.42.0 BiocGenerics_0.28.0 bindrcpp_0.2.2  Seurat_2.3.4 Matrix_1.2-15 cowplot_0.9.3  ggplot2_3.1.0