Replacing a nucleotide in a FASTA fie - r

Question

I'm trying to make fasta files for each variation of a gene using a CSV file extracted from gnoMAD. In this function,x is a list with coordinates for each variation, Y is a fasta file opened using the read.fasta function from the seqinr library and data is the file I downloaded from gnomAD. I'm having trouble with the last if statement,supposed to manage SNVs. For some reason,instead of inserting the nucleotide at the position specified, the value is concatenated at the end of the fasta file.
I've read the documentation for the library but haven't found anything about the internal representation for the fasta files.
Example of output:
t" "t" "g" "c" "t" "c" "a" "c" "a" "g" "t" "g" "t" "t" "t" "g"
"a" "g" "c" "a" "g" "t" "g" "c" "t" "g" "a" "g" "c" "a" "c" "a" "a" "a" "g" "c"
"a" "g" "a" "c" "a" "c" "t" "c" "a" "a" "t" "a" "a" "a" "t" "g" "c" "t" "a" "g"
9
"a" "t" "t" "t" "a" "c" "a" "c" "a" "c" "t" "c" "C"
The C with a 9 index should be in the ninth position of the sequence
files<-function(x,y,data){
test<-str_detect(data[ ,"Consequence"],"[del]")
names<-paste(data[ ,"Chromosome"],data[ ,"Position"],data[ ,"Reference"],data[ ,"Alternate"],"ACE2",sep="-")
for (j in 1:length(x)){
copy<-y
if(length(x[[j]])!=1 && test[j]==TRUE){
for(i in x[[j]][1]:x[[j]][2]){
copy[[1]][i]<-NA
}
copy<-copy[[1]][!is.na(copy[[1]])]
}
if(length(x[[j]])==1 && test[j]==TRUE){
copy[[1]][x[[j]][1]]<-NA
copy<-copy[[1]][!is.na(copy[[1]])]
}
if(test[j]==FALSE){
n<-x[[j]][1]
copy[[1]][n]<-complementary(data[j,"Alternate"])
print(copy[[1]][n])
}
putz<-paste(names[j],"fasta",sep=".")
write.fasta(copy,names[j],putz)
}
}