inspect

Prints a summary of a MuData file. Reads the file only; nothing is written.

mosa inspect --input <data>.h5mu

Outputs¶

MuData: 40 samples x 2 modalities
  File: <data>.h5mu

Modalities:
  gexp: 120 features | 35/40 samples present, 87.5% values non-missing | min=-1.8, mean=6, max=12.5
  meth: 80 features | 34/40 samples present, 85.0% values non-missing | min=0.000108, mean=0.495, max=1

Sample metadata (obs):
  model_type: Cell_Line: 22, Organoid: 10, Tumour: 8
  tissue: Lung: 14, Breast: 13, Colon: 13
  has_gexp: True: 40
  has_meth: True: 34, False: 6

Sample IDs (first 5): SIDM00000, SIDM00001, SIDM00002, SIDM00003, SIDM00004  ... (40 total)

Per-view sample presence:
  gexp: 35/40 samples
  meth: 34/40 samples

Per view: feature count, how many samples hold at least one observed value, the fraction of observed entries, and the range of finite values. Per metadata column: category counts, or min/mean/max for numeric columns.

MuData calls views modalities, which is the word its own output uses.

Two warnings are raised inline: a view where no sample is present, and a view whose values are all approximately zero.

inspect looks for a layer named literally mask. A file using a different name, set through data.mask_layer_name, loads and trains normally, but is reported here as having no mask layer.

The names printed here are what data.views must contain.

Note: "samples present" counts samples with real values, which can be fewer than the has_<view> count. A sample can appear in a view's file with no values recorded. See Preparing data.