#' bacterialDinucleotideFormat Function
#'
#' @param bac The bacterial file formatted by bacterialColumnNames
#' @keywords reformat the bacterial data
#' @export
#' @examples
#' bacterialDinucleotideFormat()
bacterialDinucleotideFormat <- function(bac = bacterial){
lookup_list = c("AA", "AC", "GT", "AG", "CC", "TT", "CG", "GG", "GC",
"AT", "GA", "TG", "CT", "CA", "TC", "TA")
test_list <- match(lookup_list, colnames(bac))
if(anyNA(test_list) == FALSE){
bacterialLength <- nrow(bac)
bacDinucleotide <- data.frame(genera = rep(NA, 1), dinucleotide = rep(NA, 1), prop = rep(NA, 1))
for(i in 69:84){
genera = bac[,2]
dinucleotide = rep(colnames(bac)[i], bacterialLength)
prop = bac[,i]
df <- data.frame(genera = genera, dinucleotide = dinucleotide, prop = prop)
bacDinucleotide <- bacDinucleotide%>%bind_rows(df)
}
bacDinucleotide <- bacDinucleotide%>%
mutate(type = rep("bacteria", nrow(bacDinucleotide)))%>%
filter(!is.na(dinucleotide))
bacDinucleotide <- bacDinucleotide%>%group_by(dinucleotide)%>%summarise(bac_prop = mean(prop))
return(bacDinucleotide)
}else{
NAindex <- which(is.na(test_list))
missingAA <- lookup_list[NAindex]
print("Error: Columns are missing")
print(missingAA)
}
}
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