getOrthoWeights: Convert orthologous relationships to edgelist

In mzinkgraf/fastOC: Co-expression network analysis across multiple species

Description

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

Usage

getOrthoWeights(ortho, GeneMeta, couple_const=1)

Arguments

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

Author(s)

Matthew Zinkgraf, [e-mail] #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)

References

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

mzinkgraf/fastOC documentation built on May 13, 2019, 3:01 a.m.