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Annotations (common)

"Annotations" is a general term for platforms (e.g. mRNA platforms) and other ancillary data that needs to be loaded before the experiment data for a certain high dimensional type. The annotation is generally not specific to a certain dataset, and can be shared between two or more similar datasets.

For historical reasons, parameter files named annotation.params refer to mRNA platforms. But you should prefer to use the mrna_annotation.params name for new files instead.

Parameters

  • PLATFORM Mandatory. The identifier for the annotation. The name is perhaps too specific. It should generally correspond to the name of the parent directory of the parameters file. However, unlike STUDY_ID, it is not inferred.
  • TITLE Mandatory. A human readable title for the annotation.
  • ANNOTATIONS_FILE Mandatory. Either a full path to a TSV file or the name of TSV file under a directory that is a sibling of the parameters file and has the same name as the parameters file, minus its extension.
  • ORGANISM Default: Homo Sapiens. The scientific name of the species the annotation is associated with.
  • GENOME_RELEASE Mandatory if platform contains chromosomal region information. The genome build if applicable (e.g. hg19).