getQAStats {QUALIFIER} | R Documentation

## Get statistics from gated data for QA check.

### Description

`getQAStats` calculates and extract statistics of each gated cell population in the gating hierarchies generated by flowWorkspace package.

### Usage

    getQAStats(obj, ...)

### Arguments

`obj` | A `gating hierarchy` that stores the gated cell populations for one FCS file; or a `GatingSet` or a `GatingSetList` containing multiple `gating hierarchies` or an `environment` that stores the `GatingSet` and all other information.
`...` | other arguments isFlowCore: A `logical` scalar indicating whether the statistics are the original ones in flowJo xml workspace or the re-calculated version by flowCore in R. isMFI a `logical` flag indicating whether to calculate MFI which causes the reading of raw data isSpike a `logical` flag indicating whether to calculate spike for each channel which causes the reading of raw data isRaw `logical` whether to calculate the MFI value in raw scale. pops a `numeric` or `character` vector as the population indices specifing a subset of populations to extract stats from isChannel a `logical` flag indicating whether to extract channel information from 1d gates in order to perform channel-specific QA nslaves: An `integer` scalar indicating the number of nodes. It is used for parallel computing when obj is `GatingHierarchy` or `GatingSet`. When the `parallel` package is loaded and nslaves is NULL, its value is automatically decided by available number of nodes. When it is set to 1, then forced to run in serial mode.

### Details

This is the second preprocessing step followed by parsing gating template from flowJo workspace with `flowjo_to_gatingset`. Different QA checks can be performed after this step is done. when obj is an `environment` the results are stored as a dataframe with the name of "statsOfGS" in the environment.

### Value

a data frame when obj is a `GatingHierarchy` or `GatingSet`

### Author(s)

Mike Jiang,Greg Finak

Maintainer: Mike Jiang <wjiang2@fhcrc.org>

### See Also

`qaCheck`,`qaTask`,`qaReport`

### Examples

    ## Not run:

     getQAStats(G[[1]])#extract stats from a gating hierarchy
     getQAStats(G[[1]], isMFI = TRUE, pops = c("/boundary/lymph/CD3/CD4"))#extract stats from a gating hierarchy
     getQAStats(G)#from a gating set

    ## End(Not run)

[Package QUALIFIER version 1.29.1 Index]