R: Get statistics from gated data for QA check.

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 parseWorkspace. 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>

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 1.24.1 Index]