Subject Sample Mapping
This is the mapping file format:
The first row is skipped. It must be present, otherwise the first assay will be ignored.
STUDY_IDis required, but must match the
SUBJECT_IDis the subject id. Must match the one provided in the clinical data set.
SAMPLE_CDis the name of the assay (here synonymous with "sample"). Required.
PLATFORMis the GPL id of the corresponding platform. Must be given; the platform must have already been loaded; must be the same for all rows. The value will be uppercased. It will be used to replace the
SAMPLE_TYPEwill be used to fill
de_subject_sample_mapping. It will also be used to replace the placeholder
TISSUE_TYPEwill be used to fill
tissue_type. It will also be used to replace the placeholder
TIME_POINTwill be used to fill
timepoint. It will be used to replace the
ATTR2(legacy) placeholder in
CATGEORY_CDwill be used to form the concept path for the node to be created. Components of the path are separated with
+. It can include several placeholders (see the descriptions of the other columns). In principle it can differ among the several assays, but that code path has never been tested.
SOURCE_CDis ignored (must be present as a last column).