diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..5baa8ba
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,7 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^doc$
+^Meta$
+.gitignore
+readme.md
+readme.Rmd
\ No newline at end of file
diff --git a/DESCRIPTION b/DESCRIPTION
index c9f813a..f2778f9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: cytoqc
 Type: Package
-Title: Quality control for cytometry
-Version: 0.99.1
-Author: Mike Jiang, Jake Wagner
+Title: Quality control and standardization of cytometry data
+Version: 0.99.2
+Author: Mike Jiang, Jake Wagner, Greg Finak
 Maintainer: Mike Jiang <wjiang2@fhcrc.org>
-Description: Provides quality control and quality assessment tools for cytometry data. 
+Description: Provides quality control, quality assessment, and data standardization tools for cytometry. 
 Depends: R (>= 3.5.0)
 Imports: 
     methods,
@@ -20,9 +20,11 @@ Imports:
     purrr,
     shiny,
     tibble,
-    tidyr
+    tidyr,
+    stats,
+    graphics
 License: Artistic-2.0
-biocViews: ImmunoOncology, Infrastructure, FlowCytometry, CellBasedAssays
+biocViews: Infrastructure, FlowCytometry, CellBasedAssays
 Suggests: 
     rmarkdown
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 284446e..f09485c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -84,6 +84,7 @@ importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
 importFrom(flowCore,parameters)
+importFrom(flowCore,write.FCS)
 importFrom(flowWorkspace,colnames)
 importFrom(ggcyto,autoplot)
 importFrom(ggplot2,aes)
@@ -93,6 +94,7 @@ importFrom(ggplot2,geom_jitter)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,scale_color_identity)
+importFrom(graphics,abline)
 importFrom(kableExtra,cell_spec)
 importFrom(kableExtra,collapse_rows)
 importFrom(kableExtra,column_spec)
@@ -100,6 +102,7 @@ importFrom(kableExtra,kable_styling)
 importFrom(kableExtra,row_spec)
 importFrom(knitr,kable)
 importFrom(knitr,knit_print)
+importFrom(methods,is)
 importFrom(purrr,map)
 importFrom(purrr,map_dfr)
 importFrom(purrr,reduce)
@@ -114,6 +117,14 @@ importFrom(shiny,renderPlot)
 importFrom(shiny,selectInput)
 importFrom(shiny,shinyApp)
 importFrom(shiny,wellPanel)
+importFrom(stats,dbeta)
+importFrom(stats,dt)
+importFrom(stats,mad)
+importFrom(stats,median)
+importFrom(stats,optim)
+importFrom(stats,pbeta)
+importFrom(stats,pnorm)
+importFrom(stats,pt)
 importFrom(tibble,add_row)
 importFrom(tibble,as.tibble)
 importFrom(tibble,tibble)
@@ -122,3 +133,4 @@ importFrom(tidyr,pivot_wider)
 importFrom(tidyr,separate)
 importFrom(tidyr,separate_rows)
 importFrom(tidyr,unite)
+importFrom(utils,adist)
diff --git a/R/cqc_find_reference.R b/R/cqc_find_reference.R
index 696dce2..dacb183 100644
--- a/R/cqc_find_reference.R
+++ b/R/cqc_find_reference.R
@@ -48,7 +48,7 @@ cqc_find_params_reference <- function(cqc_cf_list, type = c("channel", "marker")
 cqc_remove_not_in_reference <- function(x, ...)UseMethod("cqc_remove_not_in_reference")
 #' @importFrom flowWorkspace colnames
 #' @export
-cqc_remove_not_in_reference.cqc_report_channel <- function(x, cqc_cf_list){
+cqc_remove_not_in_reference.cqc_report_channel <- function(x, cqc_cf_list,...){
   for(sn in names(x))
   {
     check_result <- x[[sn]]
@@ -65,7 +65,7 @@ cqc_remove_not_in_reference.cqc_report_channel <- function(x, cqc_cf_list){
   }
 }
 #' @export
-cqc_remove_not_in_reference.cqc_report_marker <- function(x, cqc_cf_list){
+cqc_remove_not_in_reference.cqc_report_marker <- function(x, cqc_cf_list,...){
   for(sn in names(x))
   {
     check_result <- x[[sn]]
diff --git a/R/cqc_find_solution.R b/R/cqc_find_solution.R
index bec69a7..91c7cc4 100644
--- a/R/cqc_find_solution.R
+++ b/R/cqc_find_solution.R
@@ -31,16 +31,19 @@ cqc_find_solution.cqc_match_result_keyword <- function(x, ...){
 #' Find solution to resolve the discrepancy discovered by match_reference
 #'
 #' It tries to find the aproximate match(based on 'agrep') between the target and reference as well as the extra redundunt items that can be removed.
-#'
+#' @name cqc_find_solution
 #' @return a table (with 'from' and 'to' columns) represents the itemized fix recommendation. When 'to' is 'NA', it means the entry is redundunt and can be removed
 #' @examples
 #' \dontrun{
 #' solution <-  cqc_find_solution(groups, select = c(1, 4))
 #' }
+#' @param x A CQC object of some kind. See vignettes.
 #' @param max.distance Maximum distance allowed for a match. See ?agrep
+#' @param ... additional arguments not for the user. 
 #' @importFrom tibble tibble add_row
+#' @importFrom utils adist
 #' @export
-cqc_find_solution.cqc_match_result <- function(x, max.distance = 0.1){
+cqc_find_solution.cqc_match_result <- function(x, max.distance = 0.1,...){
   res <- map_dfr(x, function(check_result)
   {
     unknown <- check_result[["unknown"]]
diff --git a/R/cqc_fix.R b/R/cqc_fix.R
index 0ae282c..3684278 100644
--- a/R/cqc_fix.R
+++ b/R/cqc_fix.R
@@ -6,10 +6,10 @@ cqc_fix <- function(x, ...)UseMethod("cqc_fix")
 #'
 #' Peform the actual fixing action (i.e update or delete)
 #' @param x the cqc_solution returned by 'find_solution' calls
-#'
+#' @param ... addiitional arguments not for the user.
 #' @importFrom dplyr rowwise do
 #' @export
-cqc_fix.cqc_solution <- function(x, func){
+cqc_fix.cqc_solution <- function(x,...){
   group <- attr(x, "group")
   cqc_data <- attr(group, "data")
   type <- sub("cqc_solution_", "", class(x)[[1]])
@@ -29,7 +29,7 @@ cqc_fix.cqc_solution <- function(x, func){
 #' @export
 cqc_delete <- function(x, ...)UseMethod("cqc_delete")
 #' @export
-cqc_delete.cytoframe <- function(x, value, type){
+cqc_delete.cytoframe <- function(x, value, type, ...){
   if(type == "channel")
   {
     cols <- flowWorkspace::colnames(x)
@@ -55,7 +55,7 @@ cqc_delete.GatingSet <- function(x, ...){
 #' @export
 cqc_update <- function(x, ...)UseMethod("cqc_update")
 #' @export
-cqc_update.cytoframe <- function(x, from, to, type){
+cqc_update.cytoframe <- function(x, from, to, type,...){
   if(type == "channel")
   {
     flowWorkspace:::setChannel(x@pointer, from, to)
@@ -71,7 +71,7 @@ cqc_update.cytoframe <- function(x, from, to, type){
 
 }
 #' @export
-cqc_update.GatingSet <- function(x, from, to, type){
+cqc_update.GatingSet <- function(x, from, to, type,...){
   if(type == "channel")
     gs_update_channels(x, map = data.frame(old = from
                                            , new = to
diff --git a/R/cqc_group.R b/R/cqc_group.R
index 19a181e..0a9b1b9 100644
--- a/R/cqc_group.R
+++ b/R/cqc_group.R
@@ -29,7 +29,7 @@ cqc_group.cqc_gs_list <- function(x, ...){
   attr(res, "data") <- x
   res
 }
-#' QC check
+#' Perform a QC check on flow data.
 #'
 #' This is the first step of the entire qc workflow.
 #' It extracts meta information(specified by 'type' argument) from the raw data
@@ -40,6 +40,7 @@ cqc_group.cqc_gs_list <- function(x, ...){
 #' @param x cqc_cf_list
 #' @param type specify the qc type, can be "channel", "marker" or "panel"
 #' @param delimiter a special character used to separate channel and marker
+#' @param ... additional arguments.
 #' @examples
 #' \dontrun{
 #' groups <- cqc_group(cqc_cf_list, "channel")
@@ -47,7 +48,7 @@ cqc_group.cqc_gs_list <- function(x, ...){
 #' @export
 #' @importFrom dplyr filter arrange pull mutate group_indices distinct count add_count
 #' @importFrom tidyr separate separate_rows
-cqc_group.cqc_cf_list <- function(x, type = c("channel", "marker", "panel", "keyword"), delimiter = "|"){
+cqc_group.cqc_cf_list <- function(x, type = c("channel", "marker", "panel", "keyword"), delimiter = "|",...){
   sep <- paste0(delimiter, delimiter)#double delimiter for sep params and single delimiter for sep channel and marker
   keys <- sapply(x, function(cf){
     if(type == "keyword")
@@ -89,18 +90,19 @@ cqc_group.cqc_cf_list <- function(x, type = c("channel", "marker", "panel", "key
   res
 }
 
-#' Provide the summary view of the qc report
+#' Provide the summary view of the cqc_group report.
 #'
 #' It summarise the sample-wise qc report into group overview report for reference selection and further QC action.
 #'
 #' @param object qc table returned by 'cqc_group'
+#' @param ... Additional arguments not for the user. Ignore.
 #' @examples
 #' \dontrun{
 #' su <- summary(groups)
 #'
 #' }
 #' @export
-summary.cqc_group <- function(object){
+summary.cqc_group <- function(object,...){
   res <-  object %>%
     select(-c(object)) %>%
     distinct()
@@ -109,31 +111,33 @@ summary.cqc_group <- function(object){
 }
 
 #' @export
-diff.cqc_group_keyword <- function(x){
+diff.cqc_group_keyword <- function(x,...){
 
   diff.cqc_group(x, c("keyword"))
 }
 
 #' @export
-diff.cqc_group_channel <- function(x){
+diff.cqc_group_channel <- function(x,...){
 
   diff.cqc_group(x, c("channel"))
 }
 
 #' @export
-diff.cqc_group_marker <- function(x){
+diff.cqc_group_marker <- function(x,...){
 
   diff.cqc_group(x, c("marker"))
 }
 #' @export
-diff.cqc_group_panel <- function(x){
+diff.cqc_group_panel <- function(x,...){
 
   diff.cqc_group(x, c("channel", "marker"))
 }
 
-#' Helper function to only show the difference among qc group
+#' Display the differences among QC groups
 #'
 #' @param x the grouped summary report generated by 'summary' call on the 'cqc_group' results
+#' @param vars variable to split by. Determined automatically.
+#' @param ... Additional arguments not for the user. Ignore.
 #' @examples
 #' \dontrun{
 #' su <- summary(groups)
@@ -143,7 +147,7 @@ diff.cqc_group_panel <- function(x){
 #' @importFrom dplyr group_split inner_join anti_join
 #' @importFrom purrr reduce map map_dfr
 #' @export
-diff.cqc_group <- function(x, vars){
+diff.cqc_group <- function(x, vars, ...){
   grps <- x %>%
     group_split(group_id)
   commons <- grps %>% reduce(inner_join, by = vars)
@@ -152,13 +156,13 @@ diff.cqc_group <- function(x, vars){
     `class<-`(value = class(x))
 }
 
-#' Split the samples into groups
+#' Split the result of 'cqc_group' into groups
 #'
 #' It is used to split samples into separate groups when they can't be reconciled into the sampe group.
 #'
 #' @importFrom purrr walk
 #' @export
-split.cqc_group <- function(x){
+split.cqc_group <- function(x, f,drop=FALSE,...){
   cqc_data <- attr(x, "data")
   data_type <- class(cqc_data)
   vec <- x %>% select(c(object, group_id)) %>% distinct() %>% pull(group_id)
@@ -168,7 +172,7 @@ split.cqc_group <- function(x){
   })
 }
 
-#' Helper function to remove the outlier groups that can't be fixed
+#' Remove outlier groups from the result of 'cqc_group'.
 #'
 #' @param groups the object returned by 'cqc_groups'
 #' @param id the group id to be dropped from the dataset
@@ -184,7 +188,7 @@ cqc_drop_groups <- function(groups, id){
   groups
 }
 
-#' Helper function to extract the data from 'cqc_groups' object
+#' Extract the data from the result of a 'cqc_groups' call.
 #'
 #' @param groups the object returned by 'cqc_groups'
 #' @param id the group id to be selected from the dataset, default is NULL, meaning all data
@@ -198,9 +202,9 @@ cqc_get_data <- function(groups, id = NULL){
   }
   cqc_data
 }
-#' set reference
+#' Set a reference sample for further QC.
 #'
-#' It is the step prior to the further qc solution finding step.
+#' This is the first step prior to finding a QC solution for a data set.
 #'
 #' @param x cqc report generated by 'cqc_group'
 #' @param ref specifies the reference, which can be either an integer group id or a characte vector giving the actual values of the reference
diff --git a/R/cqc_io.R b/R/cqc_io.R
index 3a3fac0..6edb448 100644
--- a/R/cqc_io.R
+++ b/R/cqc_io.R
@@ -1,6 +1,9 @@
 #' Load FCS files
-#' load fcs into 'cqc_cf_list' object which is a list of cytoframes
+#' load fcs into 'cqc_cf_list' object which is a list of cytoframes.
+#' This is the method to construct the core data object for cytoQC.
+#' @param is_h5 \code{logical} should the cytoframe be constructed as an h5 disk-backed structure. Default \code{TRUE}.
 #' @import flowWorkspace
+#' @importFrom methods is
 #' @export
 cqc_load_fcs <- function(files, is_h5 = TRUE, ...){
   res <- sapply(files, function(file)load_cytoframe_from_fcs(file, is_h5 = is_h5, ...))
@@ -10,7 +13,7 @@ cqc_load_fcs <- function(files, is_h5 = TRUE, ...){
 
 #' Construct a 'cqc_cf_list' object from a list of 'cytoframe' objects
 #'
-#' For the methods dispatching purpose
+#' This is the core data object for CytoQC.
 #'
 #' @param x a list of 'cytoframe' objects
 #' @export
@@ -32,11 +35,13 @@ cqc_cf_list <- function(x){
 #' @export
 write_fcs <- function(x, ...)UseMethod("write_fcs")
 
-#' The helper function to write the cleaned cqc_cf_list back to fcs
+#' Write out tidied flow data (cqc_cf_list) back to fcs
 #' @param x cqc_cf_list
+#' @param ... additional arguments.
 #' @param out the output directory that the FCS will be written
+#' @importFrom flowCore write.FCS
 #' @export
-write_fcs.cqc_cf_list <- function(x, out, verbose = TRUE){
+write_fcs.cqc_cf_list <- function(x, out, verbose = TRUE,...){
   if(!dir.exists(out))
     dir.create(out)
   for(sn in names(x))
diff --git a/R/outlier.R b/R/outlier.R
index 4b94ab0..2c95240 100644
--- a/R/outlier.R
+++ b/R/outlier.R
@@ -21,11 +21,13 @@
 #'@author Mike Jiang,Greg Finak
 #'
 #'Maintainer: Mike Jiang <wjiang2@@fhcrc.org>
-#'@seealso \code{\link{qaCheck}},\code{\link[QUALIFIER:qaReport]{qaReport}}
+#'@seealso \code{\link[QUALIFIER:qaCheck]{qaCheck}},\code{\link[QUALIFIER:qaReport]{qaReport}}
 #'@keywords functions
-#' @rdname outlierFunctions
-#' @export
-#' @aliases rlm outlierFunctions
+#'@importFrom graphics abline
+#'@importFrom stats dbeta dt mad median optim pbeta pnorm pt
+#'@rdname outlierFunctions
+#'@export
+#'@aliases rlm outlierFunctions
 proportion.outliers.robust<-function (x, alpha = 0.01,isUpper=TRUE,isLower=TRUE)
 {
 	outliers<-rep(FALSE,length(x))
diff --git a/R/print.R b/R/print.R
index 69fdb7d..6e45eb2 100644
--- a/R/print.R
+++ b/R/print.R
@@ -1,5 +1,5 @@
 #' @export
-print.cqc_cf_list <- function(x){
+print.cqc_cf_list <- function(x,...){
   cat("cytoqc data: \n")
   cat(length(x), " samples \n")
 }
diff --git a/man/cqc_cf_list.Rd b/man/cqc_cf_list.Rd
index a033c61..f06f7e3 100644
--- a/man/cqc_cf_list.Rd
+++ b/man/cqc_cf_list.Rd
@@ -10,5 +10,5 @@ cqc_cf_list(x)
 \item{x}{a list of 'cytoframe' objects}
 }
 \description{
-For the methods dispatching purpose
+This is the core data object for CytoQC.
 }
diff --git a/man/cqc_drop_groups.Rd b/man/cqc_drop_groups.Rd
index 41be46b..b63e84b 100644
--- a/man/cqc_drop_groups.Rd
+++ b/man/cqc_drop_groups.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/cqc_group.R
 \name{cqc_drop_groups}
 \alias{cqc_drop_groups}
-\title{Helper function to remove the outlier groups that can't be fixed}
+\title{Remove outlier groups from the result of 'cqc_group'.}
 \usage{
 cqc_drop_groups(groups, id)
 }
@@ -12,5 +12,5 @@ cqc_drop_groups(groups, id)
 \item{id}{the group id to be dropped from the dataset}
 }
 \description{
-Helper function to remove the outlier groups that can't be fixed
+Remove outlier groups from the result of 'cqc_group'.
 }
diff --git a/man/cqc_find_solution.cqc_match_result.Rd b/man/cqc_find_solution.Rd
similarity index 82%
rename from man/cqc_find_solution.cqc_match_result.Rd
rename to man/cqc_find_solution.Rd
index a5a2a67..a9e07ab 100644
--- a/man/cqc_find_solution.cqc_match_result.Rd
+++ b/man/cqc_find_solution.Rd
@@ -1,13 +1,18 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cqc_find_solution.R
-\name{cqc_find_solution.cqc_match_result}
+\name{cqc_find_solution}
+\alias{cqc_find_solution}
 \alias{cqc_find_solution.cqc_match_result}
 \title{Find solution to resolve the discrepancy discovered by match_reference}
 \usage{
-\method{cqc_find_solution}{cqc_match_result}(x, max.distance = 0.1)
+\method{cqc_find_solution}{cqc_match_result}(x, max.distance = 0.1, ...)
 }
 \arguments{
+\item{x}{A CQC object of some kind. See vignettes.}
+
 \item{max.distance}{Maximum distance allowed for a match. See ?agrep}
+
+\item{...}{additional arguments not for the user.}
 }
 \value{
 a table (with 'from' and 'to' columns) represents the itemized fix recommendation. When 'to' is 'NA', it means the entry is redundunt and can be removed
diff --git a/man/cqc_fix.cqc_solution.Rd b/man/cqc_fix.cqc_solution.Rd
index 7a97829..a0095a1 100644
--- a/man/cqc_fix.cqc_solution.Rd
+++ b/man/cqc_fix.cqc_solution.Rd
@@ -4,10 +4,12 @@
 \alias{cqc_fix.cqc_solution}
 \title{Apply the cqc_solution}
 \usage{
-\method{cqc_fix}{cqc_solution}(x, func)
+\method{cqc_fix}{cqc_solution}(x, ...)
 }
 \arguments{
 \item{x}{the cqc_solution returned by 'find_solution' calls}
+
+\item{...}{addiitional arguments not for the user.}
 }
 \description{
 Peform the actual fixing action (i.e update or delete)
diff --git a/man/cqc_get_data.Rd b/man/cqc_get_data.Rd
index 412fb8c..091a8f4 100644
--- a/man/cqc_get_data.Rd
+++ b/man/cqc_get_data.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/cqc_group.R
 \name{cqc_get_data}
 \alias{cqc_get_data}
-\title{Helper function to extract the data from 'cqc_groups' object}
+\title{Extract the data from the result of a 'cqc_groups' call.}
 \usage{
 cqc_get_data(groups, id = NULL)
 }
@@ -12,5 +12,5 @@ cqc_get_data(groups, id = NULL)
 \item{id}{the group id to be selected from the dataset, default is NULL, meaning all data}
 }
 \description{
-Helper function to extract the data from 'cqc_groups' object
+Extract the data from the result of a 'cqc_groups' call.
 }
diff --git a/man/cqc_group.cqc_cf_list.Rd b/man/cqc_group.cqc_cf_list.Rd
index 82d199c..aff2f8e 100644
--- a/man/cqc_group.cqc_cf_list.Rd
+++ b/man/cqc_group.cqc_cf_list.Rd
@@ -2,12 +2,13 @@
 % Please edit documentation in R/cqc_group.R
 \name{cqc_group.cqc_cf_list}
 \alias{cqc_group.cqc_cf_list}
-\title{QC check}
+\title{Perform a QC check on flow data.}
 \usage{
 \method{cqc_group}{cqc_cf_list}(
   x,
   type = c("channel", "marker", "panel", "keyword"),
-  delimiter = "|"
+  delimiter = "|",
+  ...
 )
 }
 \arguments{
@@ -16,6 +17,8 @@
 \item{type}{specify the qc type, can be "channel", "marker" or "panel"}
 
 \item{delimiter}{a special character used to separate channel and marker}
+
+\item{...}{additional arguments.}
 }
 \value{
 a tibble with 4 columns: object, qc type (e.g. channel), group_id and nobject (i.e. group count)
diff --git a/man/cqc_load_fcs.Rd b/man/cqc_load_fcs.Rd
index 8b78558..2879be9 100644
--- a/man/cqc_load_fcs.Rd
+++ b/man/cqc_load_fcs.Rd
@@ -3,11 +3,16 @@
 \name{cqc_load_fcs}
 \alias{cqc_load_fcs}
 \title{Load FCS files
-load fcs into 'cqc_cf_list' object which is a list of cytoframes}
+load fcs into 'cqc_cf_list' object which is a list of cytoframes.
+This is the method to construct the core data object for cytoQC.}
 \usage{
 cqc_load_fcs(files, is_h5 = TRUE, ...)
 }
+\arguments{
+\item{is_h5}{\code{logical} should the cytoframe be constructed as an h5 disk-backed structure. Default \code{TRUE}.}
+}
 \description{
 Load FCS files
-load fcs into 'cqc_cf_list' object which is a list of cytoframes
+load fcs into 'cqc_cf_list' object which is a list of cytoframes.
+This is the method to construct the core data object for cytoQC.
 }
diff --git a/man/cqc_set_reference.Rd b/man/cqc_set_reference.Rd
index ac293f7..ad68ec1 100644
--- a/man/cqc_set_reference.Rd
+++ b/man/cqc_set_reference.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/cqc_group.R
 \name{cqc_set_reference}
 \alias{cqc_set_reference}
-\title{set reference}
+\title{Set a reference sample for further QC.}
 \usage{
 cqc_set_reference(x, ref)
 }
@@ -15,5 +15,5 @@ cqc_set_reference(x, ref)
 the original cqc report with the reference info attached
 }
 \description{
-It is the step prior to the further qc solution finding step.
+This is the first step prior to finding a QC solution for a data set.
 }
diff --git a/man/diff.cqc_group.Rd b/man/diff.cqc_group.Rd
index 92ec1b1..c5bdcb6 100644
--- a/man/diff.cqc_group.Rd
+++ b/man/diff.cqc_group.Rd
@@ -2,15 +2,19 @@
 % Please edit documentation in R/cqc_group.R
 \name{diff.cqc_group}
 \alias{diff.cqc_group}
-\title{Helper function to only show the difference among qc group}
+\title{Display the differences among QC groups}
 \usage{
-\method{diff}{cqc_group}(x, vars)
+\method{diff}{cqc_group}(x, vars, ...)
 }
 \arguments{
 \item{x}{the grouped summary report generated by 'summary' call on the 'cqc_group' results}
+
+\item{vars}{variable to split by. Determined automatically.}
+
+\item{...}{Additional arguments not for the user. Ignore.}
 }
 \description{
-Helper function to only show the difference among qc group
+Display the differences among QC groups
 }
 \examples{
 \dontrun{
diff --git a/man/outlierFunctions.Rd b/man/outlierFunctions.Rd
index fe74ebe..6bf9e70 100644
--- a/man/outlierFunctions.Rd
+++ b/man/outlierFunctions.Rd
@@ -67,7 +67,7 @@ Distribution based outlier detection functions.
 These different outlier detection functions are used together with qaCheck method to perform outlier checks.
 }
 \seealso{
-\code{\link{qaCheck}},\code{\link[QUALIFIER:qaReport]{qaReport}}
+\code{\link[QUALIFIER:qaCheck]{qaCheck}},\code{\link[QUALIFIER:qaReport]{qaReport}}
 }
 \author{
 Mike Jiang,Greg Finak
diff --git a/man/split.cqc_group.Rd b/man/split.cqc_group.Rd
index 453276d..2221868 100644
--- a/man/split.cqc_group.Rd
+++ b/man/split.cqc_group.Rd
@@ -2,9 +2,9 @@
 % Please edit documentation in R/cqc_group.R
 \name{split.cqc_group}
 \alias{split.cqc_group}
-\title{Split the samples into groups}
+\title{Split the result of 'cqc_group' into groups}
 \usage{
-\method{split}{cqc_group}(x)
+\method{split}{cqc_group}(x, f, drop = FALSE, ...)
 }
 \description{
 It is used to split samples into separate groups when they can't be reconciled into the sampe group.
diff --git a/man/summary.cqc_group.Rd b/man/summary.cqc_group.Rd
index fb7dd4d..28edc0b 100644
--- a/man/summary.cqc_group.Rd
+++ b/man/summary.cqc_group.Rd
@@ -2,12 +2,14 @@
 % Please edit documentation in R/cqc_group.R
 \name{summary.cqc_group}
 \alias{summary.cqc_group}
-\title{Provide the summary view of the qc report}
+\title{Provide the summary view of the cqc_group report.}
 \usage{
-\method{summary}{cqc_group}(object)
+\method{summary}{cqc_group}(object, ...)
 }
 \arguments{
 \item{object}{qc table returned by 'cqc_group'}
+
+\item{...}{Additional arguments not for the user. Ignore.}
 }
 \description{
 It summarise the sample-wise qc report into group overview report for reference selection and further QC action.
diff --git a/man/write_fcs.cqc_cf_list.Rd b/man/write_fcs.cqc_cf_list.Rd
index 3f5d330..5521944 100644
--- a/man/write_fcs.cqc_cf_list.Rd
+++ b/man/write_fcs.cqc_cf_list.Rd
@@ -2,15 +2,17 @@
 % Please edit documentation in R/cqc_io.R
 \name{write_fcs.cqc_cf_list}
 \alias{write_fcs.cqc_cf_list}
-\title{The helper function to write the cleaned cqc_cf_list back to fcs}
+\title{Write out tidied flow data (cqc_cf_list) back to fcs}
 \usage{
-\method{write_fcs}{cqc_cf_list}(x, out, verbose = TRUE)
+\method{write_fcs}{cqc_cf_list}(x, out, verbose = TRUE, ...)
 }
 \arguments{
 \item{x}{cqc_cf_list}
 
 \item{out}{the output directory that the FCS will be written}
+
+\item{...}{additional arguments.}
 }
 \description{
-The helper function to write the cleaned cqc_cf_list back to fcs
+Write out tidied flow data (cqc_cf_list) back to fcs
 }
diff --git a/vignettes/qc-gs.Rmd b/vignettes/qc-gs.Rmd
index e20dbf7..b1bc46b 100644
--- a/vignettes/qc-gs.Rmd
+++ b/vignettes/qc-gs.Rmd
@@ -3,7 +3,7 @@ title: A QC tool for openCyto
 output: rmarkdown::html_vignette
 always_allow_html: yes
 vignette: >
-  %\VignetteIndexEntry{cytoqc}
+  %\VignetteIndexEntry{cytoqc-gs}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -20,8 +20,7 @@ library(kableExtra)
 ```{r}
 library(flowCore)
 library(flowWorkspace)
-# library(cytoqc)
-devtools::load_all("../")
+library(cytoqc)
 ```
 
 ```{r include=FALSE}
diff --git a/vignettes/qc-keywords.Rmd b/vignettes/qc-keywords.Rmd
index 04ebd90..f536f1a 100644
--- a/vignettes/qc-keywords.Rmd
+++ b/vignettes/qc-keywords.Rmd
@@ -3,7 +3,7 @@ title: A QC tool for openCyto
 output: rmarkdown::html_vignette
 always_allow_html: yes
 vignette: >
-  %\VignetteIndexEntry{cytoqc}
+  %\VignetteIndexEntry{cytoqc-kw}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -20,8 +20,7 @@ library(kableExtra)
 ```{r}
 library(flowCore)
 library(flowWorkspace)
-# library(cytoqc)
-devtools::load_all("../")
+library(cytoqc)
 ```
 
 ```{r include=FALSE}
diff --git a/vignettes/qc-pregating.Rmd b/vignettes/qc-pregating.Rmd
index f8e7dcc..506e823 100644
--- a/vignettes/qc-pregating.Rmd
+++ b/vignettes/qc-pregating.Rmd
@@ -3,7 +3,7 @@ title: A QC tool for openCyto
 output: rmarkdown::html_vignette
 always_allow_html: yes
 vignette: >
-  %\VignetteIndexEntry{cytoqc}
+  %\VignetteIndexEntry{cytoqc-pregating}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -29,8 +29,7 @@ library(kableExtra)
 ```{r}
 library(flowCore)
 library(flowWorkspace)
-# library(cytoqc)
-devtools::load_all("../")
+library(cytoqc)
 ```
 
 ```{r include=FALSE}
diff --git a/vignettes/qc-pregating2.Rmd b/vignettes/qc-pregating2.Rmd
index 07e880c..753db6d 100644
--- a/vignettes/qc-pregating2.Rmd
+++ b/vignettes/qc-pregating2.Rmd
@@ -3,7 +3,7 @@ title: A QC tool for openCyto 2
 output: rmarkdown::html_vignette
 always_allow_html: yes
 vignette: >
-  %\VignetteIndexEntry{cytoqc2}
+  %\VignetteIndexEntry{cytoqc=pregating-alt}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 
@@ -28,8 +28,7 @@ library(kableExtra)
 ```{r}
 library(flowCore)
 library(flowWorkspace)
-# library(cytoqc)
-devtools::load_all("../")
+library(cytoqc)
 ```
 
 ```{r include=FALSE}