QUALIFIER (version 1.16.1)

qaReport: create quality assessment report

Description

create quality assessment report in HTML format, which contains the annotated svg summary plot for each QA task.

Usage

"qaReport"(obj, outDir, plotAll = FALSE, gsid = NULL, subset, ...)

Arguments

obj

A qaTask or a list of qaTask objects

outDir

A character scalar giving the output path of QA report.

plotAll

A logical scalar passed down to the plot method.

gsid

an integer that uniquely identifies a gating set object. if missing, the latest added gating set is selected.

subset

A logical expression as a filter that is passed to plot. see qaCheck for more details.

...

other arguments:

splash: A logical scalar indicating whether the QUALIFIER package splash tag 'generated by ...' should be written right after the report title.

title: A character scalar indicating the title of the report

subTitle: A character scalar indicating the subtitle of the report

Details

QA results need to be calculated by calling qaCheck method before using this function to generate meaningful report. It also reads the meta information of each QA task and generate the summary tables and svg plots. Svg plots provide tooltips containing the detail information about each sample and hyperlinks of densityplot for each individual FCS file.

See Also

qaCheck,plot

Examples

## Not run: 
# data("ITNQASTUDY")#load stats from disk
# checkListFile<-file.path(system.file("data",package="QUALIFIER"),"qaCheckList.csv.gz")
# qaTask.list<-read.qaTask(db,checkListFile)
# qaReport(qaTask.list[[1]],outDir="~/output")
# qaReport(qaTask.list[2:3],outDir="~/output")
# ## End(Not run)