## Written by Mercedeh Movassagh <mercedeh@ds.dfci.harvard.edu>, Aug 2020
#' twoTimePoint miRNA and mRNA interrelation in two timepoints
#'
#' This function uses the output of one2OneRnaMiRNA and returns a sampled from original file
#' interrelation dataframe depending on user sampling selection.
#' @param mRNA mRNA file generated from fold changes (FC) obj of the one2OneRnaMiRNA.
#' @param miRNA miRNA file generated from fold changes (FC) obj of the one2OneRnaMiRNA.
#' @return miRNA mRNA interrelation dataframe
#' @export
#' @keywords mRNA miRNA interrelation
#' @examples
#' \donttest{
#' x <- twoTimePoint(mRNA_fc2, miRNA_fc2)
#' }
twoTimePoint <- function(mRNA, miRNA) {
assertthat::assert_that(ncol(mRNA) == 1 && ncol(miRNA) == 1)
cc <- matrix(0, nrow = nrow(miRNA), ncol = nrow(mRNA))
rownames(cc) <- rownames(miRNA)
colnames(cc) <- rownames(mRNA)
for (i in seq_len(nrow(miRNA))) {
for (j in seq_len(nrow(mRNA))) {
cc[i, j] <- abs(miRNA[i, 1] - mRNA[j, 1])
}
}
mmycc <- reshape2::melt(cc)
names(mmycc) <- c("V1", "V2", "value")
mmycc$V1 <- as.character(mmycc$V1)
mmycc$V2 <- as.character(mmycc$V2)
return(as.data.frame(mmycc))
}
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