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Combine two loom files

Open MartaBenegas opened this issue 5 years ago • 0 comments

Hi, I would like to have all the expression data of two lanes in one loom file, so I've tried the combine() function. This is the information of the two loom files:

> zumis_l001
Class: loom
Filename: /home/marta/Descargas/dge_zumis/10x_zumis_bclist_l001.loom
Access type: H5F_ACC_RDWR
Attributes: last_modified, version, chunks, LOOM_SPEC_VERSION
Listing:
       name    obj_type dataset.dims dataset.type_class
  col_attrs   H5I_GROUP         <NA>               <NA>
 col_graphs   H5I_GROUP         <NA>               <NA>
     layers   H5I_GROUP         <NA>               <NA>
     matrix H5I_DATASET  870 x 23428          H5T_FLOAT
  row_attrs   H5I_GROUP         <NA>               <NA>
 row_graphs   H5I_GROUP         <NA>               <NA>
> zumis_l002
Class: loom
Filename: /home/marta/Descargas/dge_zumis/10x_zumis_bclist_l002.loom
Access type: H5F_ACC_RDWR
Attributes: last_modified, version, chunks, LOOM_SPEC_VERSION
Listing:
       name    obj_type dataset.dims dataset.type_class
  col_attrs   H5I_GROUP         <NA>               <NA>
 col_graphs   H5I_GROUP         <NA>               <NA>
     layers   H5I_GROUP         <NA>               <NA>
     matrix H5I_DATASET  864 x 23361          H5T_FLOAT
  row_attrs   H5I_GROUP         <NA>               <NA>
 row_graphs   H5I_GROUP         <NA>               <NA>

And the error message:

> combine(c(zumis_l001, zumis_l002), filename = "/home/marta/Descargas/dge_zumis/10x_zumis_bclist.loom")
Validating 2 input loom files
  |===============================================================================================================================================================================| 100%
Error in combine(c(zumis_l001, zumis_l002), filename = "/home/marta/Descargas/dge_zumis/10x_zumis_bclist.loom") : 
  Not all loom objects have the number of rows/features (MARGIN = 1)

Is this function suited for what I want to do?

Best, Marta.

MartaBenegas avatar Jun 01 '20 18:06 MartaBenegas