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#' Function to encode Correlated columns of alignment matrix with desired properties
#'
#' @param aliMat amino acid multiple sequence alignment in the form of a matrix
#' @param pIndex Amino acid property index to be encoded. It is the row number in the property data frame
#' @param propDf The amino acid property to analyse. It is row number in propertyDF data frame
#'
#' @return A matrix of input dimensions with amino acid alphabets replaced by amino acid properties of choice
#' @export
#'
#' @examples
#' aliMatLoc <- system.file("extdata", "aliMat.rda", package = "aaSEA")
#' aliMat <- readRDS(aliMatLoc)
#' matEncode(aliMat = aliMat, pIndex = 1, propDf = "Cruciani" )
matEncode <- function(aliMat, pIndex, propDf){
mycm <- matrix(data = 0, nrow = nrow(aliMat), ncol = ncol(aliMat))
pIndex <- pIndex
for (s in 1:nrow(aliMat)){
mySeq <- aliMat[s,]
for (i in 1:length(mySeq)){
for (j in colnames(propDf)){
if( j == toupper(mySeq[i])){
mycm[s,i] <- as.numeric(propDf[pIndex, j])
break
}
else
{
mycm[s,i] <- 0
}
}
}
}
return(mycm)
}
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