qaReport {QUALIFIER} | R Documentation

## create quality assessment report

### Description

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

### Usage

    ## S4 method for signature 'list'
    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.

### Author(s)

Mike Jiang,Greg Finak

Maintainer: Mike Jiang <wjiang2@fhcrc.org>

### 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)

[Package QUALIFIER version 1.29.1 Index]