Nothing
### Convert delta t to negative selection.
get.negsel <- function(b.PM, id.intercept, id.slop, aa.names, b.label,
b.ci.PM = NULL){
### Delta.t
b.negsel.PM <- b.PM[id.slop]
if(!is.null(b.ci.PM)){
b.negsel.ci.PM <- matrix(b.ci.PM[id.slop,], ncol = 2)
}
### log.mu
b.logmu.PM <- b.PM[id.intercept]
if(!is.null(b.ci.PM)){
b.logmu.ci.PM <- matrix(b.ci.PM[id.intercept,], ncol = 2)
}
b.negsel.label <- b.label
b.logmu.label <- b.label
for(i.aa in aa.names){
id.aa <- grep(paste("^", i.aa, "\\.", sep = ""), b.label)
if(any(b.negsel.PM[id.aa] > 0)){
### Delta.t
max.deltat <- max(b.negsel.PM[id.aa])
id.max <- which.max(b.negsel.PM[id.aa])
b.negsel.PM[id.aa] <- b.negsel.PM[id.aa] - max.deltat
b.negsel.PM[id.aa][id.max] <- -max.deltat
### log.mu
max.logmu <- b.logmu.PM[id.aa][id.max]
b.logmu.PM[id.aa] <- b.logmu.PM[id.aa] - max.logmu
b.logmu.PM[id.aa][id.max] <- -max.logmu
### Change C.I.
if(!is.null(b.ci.PM)){
if(length(id.aa) == 1){
### Delta.t
b.negsel.ci.PM[id.aa,] <- -b.negsel.ci.PM[id.aa,]
### log.mu
b.logmu.ci.PM[id.aa,] <- -b.logmu.ci.PM[id.aa,]
} else{
### Delta.t
tmp.ci <- matrix(b.negsel.ci.PM[id.aa,], ncol = 2)[id.max,]
b.negsel.ci.PM[id.aa,] <- b.negsel.ci.PM[id.aa,] - max.deltat
b.negsel.ci.PM[id.aa,][id.max,] <- -tmp.ci
### log.mu
tmp.ci <- matrix(b.logmu.ci.PM[id.aa,], ncol = 2)[id.max,]
b.logmu.ci.PM[id.aa,] <- b.logmu.ci.PM[id.aa,] - max.logmu
b.logmu.ci.PM[id.aa,][id.max,] <- -tmp.ci
}
}
### Replace codon name.
tmp <- .CF.GV$synonymous.codon[[i.aa]]
if(sum(id.aa) != length(tmp)){
tmp <- .CF.GV$synonymous.codon.split[[i.aa]]
}
### Delta.t
b.negsel.label[id.aa][id.max] <-
paste(i.aa, ".", tmp[length(tmp)], sep = "")
### log.mu
b.logmu.label[id.aa][id.max] <-
paste(i.aa, ".", tmp[length(tmp)], sep = "")
}
}
### Return.
if(!is.null(b.ci.PM)){
ret <- list(b.negsel.PM = b.negsel.PM, b.negsel.ci.PM = b.negsel.ci.PM,
b.negsel.label = b.negsel.label,
b.logmu.PM = b.logmu.PM, b.logmu.ci.PM = b.logmu.ci.PM,
b.logmu.label = b.logmu.label)
} else{
ret <- list(b.negsel.PM = b.negsel.PM,
b.negsel.label = b.negsel.label,
b.logmu.PM = b.logmu.PM,
b.logmu.label = b.logmu.label)
}
ret
} # End of get.negsel().
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