R/biCompare_method.R

In CorMut: Detect the correlated mutations based on selection pressure

#define classes
setClass("biCkaksCodon",
	slots=c(seq_formated="character",seq_formated02="character")
)
setClass("biCkaksAA", contains = "biCkaksCodon")
setClass("biMICodon", contains = "biCkaksCodon")
setClass("biMIAA", contains = "biCkaksCodon")
setClass("biJIAA", contains = "biCkaksCodon")
#constructors
biCkaksCodon<-function(a,b){
	new("biCkaksCodon",seq_formated=a,seq_formated02=b)
}
biCkaksAA<-function(a,b){
	new("biCkaksAA",seq_formated=a,seq_formated02=b)
}
biMICodon<-function(a,b){
	new("biMICodon",seq_formated=a,seq_formated02=b)
}
biMIAA<-function(a,b){
	new("biMIAA",seq_formated=a,seq_formated02=b)
}
biJIAA<-function(a,b){
	new("biJIAA",seq_formated=a,seq_formated02=b)
}
setGeneric("biCompare", 
	function(x, ...)
	standardGeneric("biCompare")
)
#ckaksCodon
setMethod("biCompare",signature(x="biCkaksCodon"),
	function(x){
		first=kaksCodon(x@seq_formated)
		second=kaksCodon(x@seq_formated02)
		tp01=filterSites(first)
		tp02=filterSites(second)
		newPositive=setdiff(tp02$mutation,tp01$mutation)
		oldPositive=setdiff(tp01$mutation,tp02$mutation)
		allpositive=union(tp01$mutation,tp02$mutation)
		ckaks01=ckaksCodon(x@seq_formated,kaks=FALSE,setPosition=allpositive)
		ckaks02=ckaksCodon(x@seq_formated02,kaks=FALSE,setPosition=allpositive)
		namelist01=rownames(ckaks01@ckaks)
		namelist02=rownames(ckaks02@ckaks)
		taglist=namelist01%in%allpositive
		taglist02=namelist02%in%allpositive
		result=new("biCompare",method="ckaksCodon",positiveSite01=oldPositive,positiveSite02=newPositive,
		state_1=ckaks01@ckaks[taglist,taglist],statistic_1=ckaks01@lod[taglist,taglist],state_2=ckaks02@ckaks[taglist02,taglist02],statistic_2=ckaks02@lod[taglist02,taglist02])
		return(result)
	}
)
#ckaksAA
setMethod("biCompare",signature(x="biCkaksAA"),
	function(x){
		first=kaksAA(x@seq_formated)
		second=kaksAA(x@seq_formated02)
		tp01=filterSites(first)
		tp01sup=filterSites(first,lod_cut=0)
		tp02=filterSites(second)
		tp02sup=filterSites(second,lod_cut=0)
		overlaped=intersect(tp01$mutation,tp02$mutation)
		newPositive=setdiff(tp02$mutation,tp01sup$mutation)
		oldPositive=setdiff(tp01$mutation,tp02sup$mutation)
		#allpositive=union(tp01$mutation,tp02$mutation)
		#warning
		allpositive=c(newPositive,oldPositive,overlaped)
		#allpcodon=union(tp01$position,tp02$position)
		allpositive_pos=sapply(allpositive,function(xx)c2s(s2c(xx)[2:(nchar(xx)-1)]),USE.NAMES=F)
		ckaks01=ckaksAA(x@seq_formated,kaks=FALSE,setPosition=allpositive_pos)
		ckaks02=ckaksAA(x@seq_formated02,kaks=FALSE,setPosition=allpositive_pos)
		namelist01=rownames(ckaks01@ckaks)
		namelist02=rownames(ckaks02@ckaks)
		taglist=namelist01%in%allpositive
		taglist02=namelist02%in%allpositive
		result=new("biCompare",method="ckaksAA",positiveSite01=oldPositive,positiveSite02=newPositive,
		state_1=ckaks01@ckaks[taglist,taglist],statistic_1=ckaks01@lod[taglist,taglist],state_2=ckaks02@ckaks[taglist02,taglist02],statistic_2=ckaks02@lod[taglist02,taglist02])
		return(result)
	}
)

#miCodon
setMethod("biCompare",signature(x="biMICodon"),
	function(x){
		first=kaksCodon(x@seq_formated)
		second=kaksCodon(x@seq_formated02)
		tp01=filterSites(first)
		tp02=filterSites(second)
		newPositive=setdiff(tp02$mutation,tp01$mutation)
		oldPositive=setdiff(tp01$mutation,tp02$mutation)
		allpositive=union(tp01$mutation,tp02$mutation)
		ckaks01=miCodon(x@seq_formated,kaks=FALSE,setPosition=allpositive)
		ckaks02=miCodon(x@seq_formated02,kaks=FALSE,setPosition=allpositive)
		namelist01=rownames(ckaks01@mi)
		namelist02=rownames(ckaks02@mi)
		taglist=namelist01%in%allpositive
		taglist02=namelist02%in%allpositive
		result=new("biCompare",method="miCodon",positiveSite01=oldPositive,positiveSite02=newPositive,
		state_1=ckaks01@mi[taglist,taglist],statistic_1=ckaks01@p.value[taglist,taglist],state_2=ckaks02@mi[taglist02,taglist02],statistic_2=ckaks02@p.value[taglist02,taglist02])
		return(result)
	}
)

#miAA
setMethod("biCompare",signature(x="biMIAA"),
	function(x){
		first=kaksAA(x@seq_formated)
		second=kaksAA(x@seq_formated02)
		tp01=filterSites(first)
		tp02=filterSites(second)
		newPositive=setdiff(tp02$mutation,tp01$mutation)
		oldPositive=setdiff(tp01$mutation,tp02$mutation)
		allpositive=union(tp01$mutation,tp02$mutation)
		allpcodon=union(tp01$position,tp02$position)
		ckaks01=miAA(x@seq_formated,kaks=FALSE,setPosition=allpcodon)
		ckaks02=miAA(x@seq_formated02,kaks=FALSE,setPosition=allpcodon)
		namelist01=rownames(ckaks01@mi)
		namelist02=rownames(ckaks02@mi)
		taglist=namelist01%in%allpositive
		taglist02=namelist02%in%allpositive
		result=new("biCompare",method="miAA",positiveSite01=oldPositive,positiveSite02=newPositive,
		state_1=ckaks01@mi[taglist,taglist],statistic_1=ckaks01@p.value[taglist,taglist],state_2=ckaks02@mi[taglist02,taglist02],statistic_2=ckaks02@p.value[taglist02,taglist02])
		return(result)
}
)
#jiAA
setMethod("biCompare",signature(x="biJIAA"),
	function(x){
		first=kaksAA(x@seq_formated)
		second=kaksAA(x@seq_formated02)
		tp01=filterSites(first)
		#tp01sup=filterSites(first,lod_cut=0)
		tp02=filterSites(second)
		#tp02sup=filterSites(second,lod_cut=0)
		overlaped=intersect(tp01$mutation,tp02$mutation)
		newPositive=setdiff(tp02$mutation,tp01$mutation)
		oldPositive=setdiff(tp01$mutation,tp02$mutation)
		allpositive=c(newPositive,oldPositive,overlaped)
		allmutations_pos=sapply(allpositive,function(xxx)substr(xxx,2,(nchar(xxx)-1)),USE.NAMES=F)
		#allpcodon=union(tp01$position,tp02$position)
		ckaks01=jiAA(x@seq_formated,kaks=FALSE,setPosition=allmutations_pos)
		ckaks02=jiAA(x@seq_formated02,kaks=FALSE,setPosition=allmutations_pos)
		namelist01=rownames(ckaks01@JI)
		namelist02=rownames(ckaks02@JI)
		taglist=namelist01%in%allpositive
		taglist02=namelist02%in%allpositive
		result=new("biCompare",method="jiAA",positiveSite01=oldPositive,positiveSite02=newPositive,
		state_1=ckaks01@JI[taglist,taglist],statistic_1=ckaks01@p.value[taglist,taglist],state_2=ckaks02@JI[taglist02,taglist02],
		statistic_2=ckaks02@p.value[taglist02,taglist02])
		return(result)
}
)