#' Example Absolute mRNA
#'
#' Data generated with supplemental script provided by
#' <DOI:10.1371/journal.pcbi.1004075>. Data originally
#' sourced from <DOI:10.1016/j.cell.2012.09.019>.
#' A time series of yeast mRNA abundance after removal
#' of a key nutrient. Absolute abundance estimated
#' by multiplying microarray signal (relative to first
#' time point) by the initial nCounter-calibrated and
#' copy-per-cell-adjusted RNA-seq abundance (averaged
#' across two replicates). Divide absolute abundances
#' by total sample abundance to make data relative.
#'
#' @usage data(marg.abs)
"marg.abs"
#' Ensure Matrix Has Dim Names
#'
#' Makes sure input data has correct format. For back-end use only.
#'
#' @param counts A data matrix representing counts.
#' @return A matrix with dim names.
as_safe_matrix <-
function(counts) {
if ("data.frame" %in% class(counts))
counts <- as.matrix(counts)
if (is.null(colnames(counts)))
colnames(counts) <- as.character(1:ncol(counts))
if (is.null(rownames(counts)))
rownames(counts) <- as.character(1:nrow(counts))
if (any(is.na(counts)))
stop("Remove NAs from 'counts' before proceeding.")
return(counts)
}
#' Make Progress Bar
#'
#' Makes a progress bar. For back-end use only.
#'
#' @param i The current iteration.
#' @param k Total iterations.
#' @param numTicks The result of \code{progress}.
#' @return The next \code{numTicks} argument.
progress <- function(i, k, numTicks) {
if (i == 1)
numTicks <- 0
if (numTicks == 0)
cat("|-")
while (i > numTicks * (k / 40)) {
cat("-")
if (numTicks == 10)
cat("(25%)")
if (numTicks == 20)
cat("(50%)")
if (numTicks == 30)
cat("(75%)")
numTicks <- numTicks + 1
}
if (i == k)
cat("-|\n")
return(numTicks)
}
#' Package Check
#'
#' Checks whether the user has the required package installed.
#' For back-end use only.
#'
#' @param package A character string. An R package.
#' @return Returns TRUE if no error.
packageCheck <- function(package) {
if (!requireNamespace(package, quietly = TRUE)) {
stop(
"Uh oh! This method depends on ",
package,
"! ",
"\nTry running: install.packages('",
package,
"')",
"\nor: BiocManager::install('",
package,
"')"
)
}
TRUE
}
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