#' window_size_cor function
#'
#' This function is one of the functions that makes EntropyMSA works.
#' @param MSA3 The input is a multiple sequence alignment in FASTA format.
#' @param n By default, n = 1, which means only a single character per alignment
#' column per sequence. For example, users may change to n = 9 for nonamer
#' scoring instead of monomer.
#' @param randomise This parameter allows users to try other corrected entropy
#' values. By default, set.seed is used in entropy correction and hence, same
#' values are produced, which made it easier for the empiral study to determine
#' the effects of correction in various sample and population sizes.
#' @keywords entropy
#' @export
#' @examples
#' #see EntropyMSA function
window_size_cor <- function(MSA3,n,randomise){
#character column for each column
column <- c()
#numeric vector to hold each column H bit
#H <- c()
Hcor <- c();slope <- c();r2 <- c()
for (o in seq_len(length(MSA3[[1]])-n+1)){
for (q in 1:length(MSA3)){
column <- c(column,paste(MSA3[[q]][seq(o,o+n-1)],sep="",collapse=""))
}
#H <- c(H,entropy_vect(column))
H_list_result <- resampler(column,randomise)
Hcor <- c(Hcor,H_list_result$intercept)
slope <- c(slope,H_list_result$slope)
r2 <- c(r2,H_list_result$R2)
column <- c()
}
#H
Hcor
#finalList <- list(H=Hcor,slope=slope,R2=r2)
}
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