compass.subset.comparisons: COMPASS Subset Comparisons

In seshadrilab/flowHelpers: Collection of helper functions for analyzing FCM data

Description

Obtain background-corrected proportions for COMPASS subsets. Perform Wilcoxon rank sum test comparing mean for one group to mean for another group. Defaults to only subsets above threshold 0.01. Saves a csv with the above data to the outdir, if provided.

Usage

compass.subset.comparisons(compassResultOrPath, gsOrGsListOrPath,
  parentSubset, threshold = 0.01, antigenCol, stimAntigen,
  controlAntigen, stratifyBy, outdir = NULL,
  stratifyByValueMinuend = NULL, stratifyByValueSubtrahend = NULL,
  sampleIDCol)

Arguments

compassResultOrPath
gsOrGsListOrPath
parentSubset
threshold	(optional) Filters subsets where the average mean_gamma is greater than the threshold
antigenCol
stimAntigen
controlAntigen
stratifyBy	column of pData to stratify data by
outdir	(optional)
stratifyByValueMinuend	(optional) stratifyBy value to be used as selector for minuend (A in A - B)
stratifyByValueSubtrahend	(optional) stratifyBy value to be used as selector for subtrahend (B in A - B)

Details

It is assumed that any given GatingSetList will have the same gates across all GatingSets within.

Examples

## Not run: 
ifngResults <- compass.subset.comparisons(compassResultOrPath=myCompassResult,
       gsOrGsListOrPath=gs,
       parentSubset="4+",
       antigenCol="Antigen",
       stimAntigen="Peptide Pool 1",
       controlAntigen="DMSO",
       stratifyBy="Status",
       sampleIDCol="PATIENT ID")

## End(Not run)

seshadrilab/flowHelpers documentation built on May 23, 2019, 4:05 a.m.