A named list of 5 spatial data frames, one per TMA core, in the form produced by
HALO cell phenotyping. Each has 51 columns: the sample identifier, cell
bounding-box coordinates (XMin, XMax, YMin, YMax), 12 binary
marker/phenotype indicator columns, per-marker intensity and area columns, and a
Classifier.Label column with levels Tumor and Stroma.
Format
A named list of 5 data frames, each with 51 columns:
- TMA1_[3,B].tif
3803 cells
- TMA2_[3,B].tif
3008 cells
- TMA3_[7,B].tif
1850 cells
- TMA3_[9,K].tif
1803 cells
- TMA3_[8,U].tif
2318 cells
Details
Marker positives are sparse and vary widely between cores, which matters when
choosing a core for examples or tests: TMA3_[9,K].tif has 536 CD3+ and 83 CD8+
cells, whereas TMA1_[3,B].tif has 17 and 7. Several markers are entirely
absent from some cores.
Note that deidentified_sample here is character, while deidentified_id
in example_clinical and example_summary is integer.