# Quality Control of Gated Flow Cytometry Experiments

## Documentation for package ‘QUALIFIER’ version 1.28.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

QUALIFIER-package | QUALIFIER: A package that provides automated flow data quality assessment based on gated cell populations
clearCheck | Perform the quality assessment for the qaTask object
db | The example QA data included in the package
description,qaTask | a class for storing important information of flow cytometry data quality assessment task
formula,qaTask | a class for storing important information of flow cytometry data quality assessment task
getData,qaTask | a class for storing important information of flow cytometry data quality assessment task
getName,qaTask | a class for storing important information of flow cytometry data quality assessment task
getPop,qaTask | a class for storing important information of flow cytometry data quality assessment task
getQAStats | Get statistics from gated data for QA check.
getQAStats-method | Get statistics from gated data for QA check.
getQAStats-methods | Get statistics from gated data for QA check.
highlight | a class for storing important information of flow cytometry data quality assessment task
highlight-method | a class for storing important information of flow cytometry data quality assessment task
highlight<- | a class for storing important information of flow cytometry data quality assessment task
highlight<--method | a class for storing important information of flow cytometry data quality assessment task
htmlReport | a class for storing important information of flow cytometry data quality assessment task
htmlReport-method | a class for storing important information of flow cytometry data quality assessment task
htmlReport<- | a class for storing important information of flow cytometry data quality assessment task
htmlReport<--method | a class for storing important information of flow cytometry data quality assessment task
initDB | Initializes the data environment
ITNQASTUDY | The example QA data included in the package
load_db | save/load the data environment to/from disk
outlier.cutoff | outliers detection functions
outlier.norm | outliers detection functions
outlier.t | outliers detection functions
outlierFunctions | outliers detection functions
plot | plot the statistics for a particular cell population of a group of samples
plot-method | plot the statistics for a particular cell population of a group of samples
plot-methods | plot the statistics for a particular cell population of a group of samples
plotType,qaTask | a class for storing important information of flow cytometry data quality assessment task
proportion.outliers.mle | outliers detection functions
proportion.outliers.robust | outliers detection functions
qaCheck | Perform the quality assessment for the qaTask object
qaCheck-method | Perform the quality assessment for the qaTask object
qaCheck-methods | Perform the quality assessment for the qaTask object
qaCheckList | The example QA data included in the package
qaID,qaTask | a class for storing important information of flow cytometry data quality assessment task
qaLevel,qaTask | a class for storing important information of flow cytometry data quality assessment task
qaPreprocess | Preprocessing for QA check
qaReport | create quality assessment report
qaReport-method | create quality assessment report
qaReport-methods | create quality assessment report
qaTask | a class for storing important information of flow cytometry data quality assessment task
qaTask-class | a class for storing important information of flow cytometry data quality assessment task
qoutlier | outliers detection functions
qpar | a class for storing important information of flow cytometry data quality assessment task
qpar-method | a class for storing important information of flow cytometry data quality assessment task
qpar<- | a class for storing important information of flow cytometry data quality assessment task
qpar<--method | a class for storing important information of flow cytometry data quality assessment task
QUALIFIER | QUALIFIER: A package that provides automated flow data quality assessment based on gated cell populations
queryStats | Perform the quality assessment for the qaTask object
queryStats-method | Perform the quality assessment for the qaTask object
read.qaTask | Loading 'qaTask's from a csv file
rFunc | a class for storing important information of flow cytometry data quality assessment task
rFunc-method | a class for storing important information of flow cytometry data quality assessment task
rFunc<- | a class for storing important information of flow cytometry data quality assessment task
rFunc<--method | a class for storing important information of flow cytometry data quality assessment task
rlm | outliers detection functions
saveToDB | Save the gating set and annotation data into the data environment.
save_db | save/load the data environment to/from disk
scatterPar | a class for storing important information of flow cytometry data quality assessment task
scatterPar-method | a class for storing important information of flow cytometry data quality assessment task
scatterPar<- | a class for storing important information of flow cytometry data quality assessment task
scatterPar<--method | a class for storing important information of flow cytometry data quality assessment task
show,qaTask | a class for storing important information of flow cytometry data quality assessment task
tubesevents | The example QA data included in the package