#' Get Confidence Intervals after the bootstrap procedure
#'
#'@details Extract the confidence intervals from the provided samples across all tissues
#'
#'@param x The results from \code{\link{bootMeans}}
#'@param alpha Return (1 - alpha) confidence intervals
#'@param combined Combine all Tissues within the sample
#'
#'@return Returns a \code{tbl_df} with lower, median and upper quantiles for the interval.
#'If \code{combined = TRUE} the \code{tbl_df} will only contain one row.
#'If \code{combined = FALSE} the \code{tbl_df} will contain one row per tissue.
#'
#'@author Steve Pederson
#'
#'@import dplyr
#'@import magrittr
#'
#'@rdname getCI
#'@export
getCI <- function(x, alpha, combined = FALSE){
chkNames <- x %>% # Check that all tissues have the correct structure.
vapply(function(x){
"samples" %in% names(x)
},
logical(1))
stopifnot(chkNames)
if (!combined) {
out <- x %>%
lapply(extract2, "samples") %>%
lapply(quantile, probs = c(alpha/2, 0.5, 1 - alpha/2)) %>%
lapply(t) %>%
lapply(as.data.frame) %>%
bind_rows() %>%
set_names(c("lower", "median", "upper")) %>%
mutate(Tissue = names(x))
}
else {
out <- x %>%
lapply(extract2, "samples") %>%
unlist %>%
quantile(probs = c(alpha/2, 0.5, 1 - alpha/2)) %>%
as.list %>%
as.data.frame %>%
set_names(c("lower", "median", "upper"))
}
out
}
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