cytokine.specific.subset.comparison: Cytokine-specific Subset Comparison

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

Description

Compare cytokine-positive subsets to cytokine-negative subsets. Additionally stratify by a column in the sample metadata. Perform a wilcoxon rank sum test for each subset group.

Usage

cytokine.specific.subset.comparison(compassResultOrPath, gsOrGsListOrPath,
  cytokineOfInterestGate, parentSubset, threshold = 0.01, antigenCol,
  stimAntigen, controlAntigen, stratifyBy,
  showSignificanceBracket = TRUE, showTitle = TRUE, sampleIDCol,
  outdir = NULL, themeBaseSize = 15, removeGridAndBg = FALSE,
  stratifyByColors = NULL, ymax = NULL,
  stratifyByValueMinuend = NULL, stratifyByValueSubtrahend = NULL)

Arguments

compassResultOrPath
gsOrGsListOrPath
cytokineOfInterestGate
parentSubset
threshold	(optional) Filters subsets where the average mean_gamma is greater than the threshold
antigenCol
stimAntigen
controlAntigen
stratifyBy	column of pData to stratify plot by
showSignificanceBracket	(optional)
showTitle	(optional)
outdir	(optional)
themeBaseSize	(optional)
removeGridAndBg	(optional)
stratifyByColors	(optional)
ymax	(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 <- cytokine.specific.subset.comparison(compassResultOrPath=myCompassResult,
       gsOrGsListOrPath=gs,
       cytokineOfInterestGate="IFNg+",
       parentSubset="4+",
       antigenCol="Antigen",
       stimAntigen="Peptide Pool 1",
       controlAntigen="DMSO",
       stratifyBy="Status",
       showSignificanceBracket=TRUE,
       showTitle=FALSE,
       sampleIDCol="PATIENT ID")

## End(Not run)

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