R/pairwiseSpike.R

In aryanahmad/VisualSARSDiff: Getting and Comparing Protein-Protein Interactions in SARS and others

#This is a legacy method. Comparing 2 spike proteins by pairwise sequencing
#is too restrictive, and does not provide any analyzing compared
#to protein-protein interactions that this package has evolved to.


#' #' Pairwise compare 2 spike protines
#' #'
#' #' @param spike1 A spike sequence from a FAFSA file.
#' #' @param spike2 A spike sequence from a FAFSA file.
#' #' @param scoreCheck Bool
#' #' @return the score and comparison of the 2 proteins.
#' pairwiseSpike <- function(spike1, spike2, scoreCheck) {
#'   if(is.null(spike1) || is.null(spike2) || is.null(scoreCheck)){
#'     stop()
#'   }
#'   if(spike1 == "COVID-19"){
#'     spike1 <- covid19spike
#'   }
#'   if(spike2 == "COVID-19"){
#'     spike2 <- covid19spike
#'   }
#'   if(spike1 == "MERS"){
#'     spike1 <- mersspike
#'   }
#'   if(spike2 == "MERS"){
#'     spike2 <- mersspike
#'   }
#'   spike1Sequence <- spike1[[1]]
#'   spike2Sequence <- spike2[[1]]
#'   spike1String <- c2s(spike1Sequence)
#'   spike2String <- c2s(spike2Sequence)
#'
#'   pairwiseAlignment(spike1String, spike2String, scoreOnly = scoreCheck)
#}