alter_pathway_names: alter_pathway_names

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 existing pathway names by homology pathway molecules with multiple replacement.

Usage

alter_pathway_names(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 existing pathway names by homology pathway molecules with multiple replacement.

Value

This function alters the pathway data with the existing pathways' name change 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))
human.pathway.update<-alter_pathway_names(homology.table, human.pathway)
human.pathway.update

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