getOrthoWeights: Convert orthologous relationships to edgelist

Description Usage Arguments Author(s) References

View source: R/functions.R

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

1
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, [email protected] #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 Aug. 15, 2018, 11:17 p.m.