Species: Species Overview
In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools
Species R Documentation
Species Overview
Description
Overview of 'DuffyTools' notion of Species
Details
We use the notion of 'species' to mean a single organism or strain
that has it's own unique genomic annotation. Contrast this with
Targets.
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.
To accomplish this, we need to work with multiple species in a seamless and
coordinated manner.
A species definition consists of a MapSet – a collection of objects that
completely describes the genomic annotation – and 2 unique identifiers:
a SpeciesID and a species FilePrefix. See MapSets for full
details. The SpeciesID is used to tell the software which MapSet
(annotation) to use, and the FilePrefix is used for the reading and writing
of all species-specific files. Typically, the species file prefix is a
shortened version of the SpeciesID, unique over the set of all possible
species of interest.
In the trivial case of operating on datasets from just a single species, it
is customary for the SpeciesID to exactly match the TargetID.
See Also
getCurrentSpecies, for getting details about the current species.
setCurrentSpecies, to change to a different species.
getCurrentGeneMap, to get the table of genes.
getCurrentExonMap, to get the table of coding exons.
getCurrentSeqMap, to get the table of sequences (chromosomes).
getCurrentRrnaMap, to get the table of ribosomal RNA and other
special case genes.
robertdouglasmorrison/DuffyTools documentation built on April 16, 2024, 6:31 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| Species | R Documentation |
Species Overview
Description
Overview of 'DuffyTools' notion of Species
Details
We use the notion of 'species' to mean a single organism or strain
that has it's own unique genomic annotation. Contrast this with
Targets.
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. To accomplish this, we need to work with multiple species in a seamless and coordinated manner.
A species definition consists of a MapSet – a collection of objects that
completely describes the genomic annotation – and 2 unique identifiers:
a SpeciesID and a species FilePrefix. See MapSets for full
details. The SpeciesID is used to tell the software which MapSet
(annotation) to use, and the FilePrefix is used for the reading and writing
of all species-specific files. Typically, the species file prefix is a
shortened version of the SpeciesID, unique over the set of all possible
species of interest.
In the trivial case of operating on datasets from just a single species, it is customary for the SpeciesID to exactly match the TargetID.
See Also
getCurrentSpecies, for getting details about the current species.
setCurrentSpecies, to change to a different species.
getCurrentGeneMap, to get the table of genes.
getCurrentExonMap, to get the table of coding exons.
getCurrentSeqMap, to get the table of sequences (chromosomes).
getCurrentRrnaMap, to get the table of ribosomal RNA and other
special case genes.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.