Nothing
trimAlignment <- function(alignment, perc, header, verbose){
print(paste("Trimming the alignment to", perc, "% frequency across the sequences"))
missingRes<-0
rows<- length(alignment[,1])
cols<- length(alignment[1,])
hitNum = rows-((rows*perc)/100) # number of missing elements in a column
columnsToKeep<-rep(NA, cols)
for(j in 1:cols){
for(i in 1:rows){
if ((alignment[i,j])=="*") missingRes<-missingRes+1
}
if(verbose==1) print(paste("Column", j, "of the alignements misses", missingRes))
if (missingRes >= hitNum) {if(verbose==1) print(paste("column", j, "will be discarded"))}
else{ columnsToKeep[j] <- j}
missingRes<-0
}
trimmed<-alignment[ ,columnsToKeep[!is.na(columnsToKeep)]]
names(trimmed)<-header[columnsToKeep[!is.na(columnsToKeep)]]
trimmed
}
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