#' Create conf\_filter object
#'
#' @param cmsObj an object of class 'CoreMSData', should be output of the function
#' \code{\link{as.CoreMSData}}
#'
#' @details To be used with \code{\link{applyFilt.confFilt}} to subset peaks with a minimum confidence score of \code{min_conf}
#'
#' @return object of class 'confFilt'
#'
#' @author Natalie Winans
#'
#' @export
conf_filter <- function(cmsObj) {
if(!inherits(cmsObj, "CoreMSData")) stop("cmsObj must be of class 'CoreMSData")
conf_id <- attr(cmsObj, "cnames")$conf_cname
obs_mass_id <- attr(cmsObj, "cnames")$obs_mass_cname
error_id <- attr(cmsObj, "cnames")$error_cname
file_id <- attr(cmsObj, "cnames")$file_cname
formula_id <- attr(cmsObj, "cnames")$mf_cname
moutput <- cmsObj$monoiso_data %>% dplyr::select(obs_mass_id, conf_id, error_id, formula_id, file_id)
ioutput <- cmsObj$iso_data %>% dplyr::select(obs_mass_id, conf_id, error_id, formula_id, file_id)
output <- list("monoiso_data" = moutput, "iso_data" = ioutput)
class(output) <- c("confFilt", "list")
attr(output, "conf_cname") <- conf_id
return(output)
}
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