Overview of 'DuffyTools' Target Organism(s)
We use the notion of 'target' to mean a small set of organisms or species that are to be treated as a single unit for functional genomics analysis. Our lab's focus is on host parasite interactions and most of our datasets involve measuring gene expression of both the host and the parasite in a single experiment, be it microarrays, proteomics, or NextGen sequencing.
A target definition consists of 3 parts: a TargetID, a set of 1 or more SpeciesIDs, and an equally long set of species file prefixes. In this way, the tools can operate on the datasets as a single entity while simultaneously reading, using, and creating all necessary species-specific information.
For the trivial case of a target being a single species, it is customary for the TargetID to exactly match the SpeciesID. The file prefix is typically a shortened version of the SpeciesID, with enough uniqueness over the set of all possible species of interest.
For a detailed overview of species annotations, see
for understanding the subtle difference between a target and a species,
getCurrentTarget, for getting details about the current target.
getAllTargets, for getting details about all predefined targets.
setCurrentTarget, to change the current target.
addTarget, to add a new target definition.
importTargets, to managing the
set of all known targets.
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