Description Usage Arguments Author(s) References
Generate a coupling matrix that connects species based on the orthologus relationships between species. Relationships can range from one-to-one to many-to-many
1 | getOrthoWeights(ortho, GeneMeta, couple_const=1)
|
ortho |
List object that contains the orthologous gene relationships between species |
GeneMeta |
Data frame that contains the project metadata. See createGeneMeta |
couple_const |
A contant that determines the relative contribution of orthologous gene relationships between species. Default=1 |
Matthew Zinkgraf, Matthew.Zinkgraf@wwu.edu #Create ortho data("GeneMeta") data("potri_eugra") data("potri_sapur") data("sapur_eugra")
ortho <- list(potri_eugra = potri_eugra, potri_sapur = potri_sapur, sapur_eugra = sapur_eugra)
#calculate orthologous weights ortho_weights <- getOrthoWeights(ortho, GeneMeta, couple_const = 1)
Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Chao Cheng and Mark Gerstein. 2014. OrthoClust: an orthology-based network framework for clustering data across multiple species. Genome Biology. 15:R100
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