alter_pathway_elements: alter_pathway_elements

In humayun2017/SPAGI2: SPAGI2: Identification of active signalling pathways for cross-species by integrating gene expression and human protein interaction network

Description

This function alters human pathway elements by homology molecules of other species.

Usage

alter_pathway_elements(homology.table, human.pathway)

Arguments

homology.table	Homology table for the pathway molecules of the two species - species1 and species2
human.pathway	A list with human pathway path data where each sublist denotes a path of the pathway. This is used as background data.

Details

This function alters human pathway elements by homology molecules of other species.

Value

This function returns the pathway data by altering the pathway molecules by the homology molecules.

Examples

P<-list(c('P','G','A','N'), c('P','C','X','T'), c('P','M','N','D'))
Q<-list(c('Q','M','O','T','L'), c('Q','U','T','F'), c('Q','M','N','I','B'))
R<-list(c('R','X','B','K'), c('R','G','H','O'), c('R','U','C','E'))
QQ<-list(c('Q','M','O','T','L'), c('Q','U','T','F'), c('Q','M','N','I','B'))
S<-list(c('S','M','NN'), c('S','N','O','B1'))
U<-list(c('SS','OO','nn'), c('ss','oo','hh'))
V<-list(c('V','X','B','D','J','E','K'), c('V','M','O','F','D','G'), c('V','B','C'))
human.pathway<-list("P"=P, "Q"=Q, "R"=R, "QQ"=QQ, "S"=S, "U"=U, "V"=V)
homology.table<-data.frame('human_mol'=c('B1','C','X','R',LETTERS), 'other_mol'=c('b','c1','x1','r1',letters))
homology.pathway<-alter_pathway_elements(homology.table, human.pathway)
homology.pathway

humayun2017/SPAGI2 documentation built on Aug. 5, 2020, 12:06 a.m.