#' List concatamers of selected sites for all working_swarm sequences in swarmset.
#'
#' @param x swarmset
#' @param ... not currently used by could and should be soon
#' @seealso \code{\link{swarmset}}
#'
#' @family swarmset methods
#'
#' @export
tabulate.swarmset <- function(x) {
if (class(x) != "swarmset")
stop("ERROR: please pass as swarmset object to tabulate.swarmset()")
ins <- which(x$working_swarm$is_included == T)
# name = names(x$working_swarm$dotseq_concatamer)[ins]
concatamer = x$working_swarm$dotseq_concatamer[ins]
# output the full TF concatamer sequence
i <- min(which(x$working_swarm$is_included == T))
if (!is.null(x$tf_index) & x$working_swarm$is_included[x$tf_index] &
x$tf_index != i)
i <- x$tf_index
concatamer[names(x$working_swarm$dotseq_concatamer)[i]] = seqinr::c2s(x$working_swarm$aln_concatamer[i, ])
return(data.frame(concatamer))
# message(paste0("Number of mutations to be represented was initially ",
# x$working_swarm$initial_n_variants, "."))
# if (length(which(c(x$working_swarm$variant_counts) > 0)) == 0) {
# message("Number of mutations to be represented is now 0.")
# } else {
# message("Missed:")
# pos.counts <- apply(x$working_swarm$variant_counts, 2, max)
# r=1
# for (i in which(pos.counts > 0)) {
# for (j in which(x$working_swarm$variant_counts[, i] > 0)) {
# message(paste(r, "\t",
# paste(colnames(x$working_swarm$dot_concatamer)[i],
# rownames(x$working_swarm$variant_counts)[j], sep='')))
# r=r+1
# }
# }
# }
}
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