R/cytoqc-package.R

In RGLab/cytoqc: Quality control and standardization of cytometry data

#' @keywords internal
#' @details
#' The cytoqc package is used to perform QC and data standardization for flow and mass cytometry data stored in
#' GatingSet objects or FCS files.
#'
#' It simplifies the tasks of standardizing channel, markers, keywords, gating schemes, gate names, and so forth, necessary to
#' run cytometry data through automated analysis pipelines.
#'
#' The process for running cytoqc from FCS files consists of several steps.
#'
#' First, one loads the data from FCS files using  \code{cqc_load_fcs()}.
#' The data is loaded into a \code{cqc_cf_list} object.
#'
#' Next a QC evaluation of  "channel", "marker" or "panel" is performed using \code{cqc_check()}.
#' This returns a \code{cqc_check} family object, specific to either the "channel", "marker" or "panel" qc.
#' This object can be viewed using \code{summary}.
#' A nice print out of the \code{cqc_check} for reports can be generated with \code{knit_print}.
#'
#' Next a reference group is chosen using \code{cqc_match()} and passing in a vector of channels or markers to use as the referece.
#' Alterately one can pass in the group_id of the group to use as a reference.
#' This returns a \code{cqc_match_result}.
#'
#' Next we resolve discrepancies using \code{cqc_recommend} on the \code{cqc_match_result}.
#' This will propose several ways to resolve discrepancies in the markers, channels, or panel.
#' Again, a pretty print out can be generated using \code{knit_print}.
#'
#' Finally the proppsed solution can either be edited (by writing it out to a csv file and editing it), or by applying \code{cqc_fix()} to the \code{cqc_solution}.
#'
#' The QC can be updated after applying the fix using \code{cqc_check} again.
#'
#' Any groups that cannot be standardized can be dropped using \code{cqc_drop_groups}.
#'
#' The tidied data can be coerced to a \code{cytoset} via a call to the \code{cytoset()} constructor.
#'
#' To summarize:
#' Read -> group -> set reference -> propose a solution to qc issues -> apply the solution -> store cleaned data.
#'
#' See the different vignettes for additional details.
#'
"_PACKAGE"

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