idFeaturesByBackgating: (Internal use only) Identify features of flow cytometry data...

In RGLab/flowStats: Statistical methods for the analysis of flow cytometry data

(Internal use only) Identify features of flow cytometry data using backgating

Description

Identify and labeling significant features using divisive clustering method such as diana.

Usage

idFeaturesByBackgating(bg, nDim, thres.sigma=2.5, lambda=0.1,
                       reference.method="median",
                       plot.workflow=FALSE, ask=names(dev.cur())!="pdf")

Arguments

bg	A data frame containing subpopulations on channels of interests. Must be a returning result from flowStats:::backGating
nDim	An integer indicating the length of channels of interest.
thres.sigma	An numerical value indicating the threshold at which to cut tree, e.g., as resulting from 'diana', into several clusters.
lambda	A numerical value indicating the percentage of the potential features that is used as a threshold for deciding outlier clusters. The default value is 0.1.
reference.method	A character vector indicating the method for computing the reference features. If median, the reference feature is defined by the medain of eac cluster of features. Valid methods include median and mean only.
plot.workflow	Logical. If TURE, display the workflow of feature identification.
ask	Logical. If TRUE, the display operates in interactive mode.

Details

Using the resulting data frame from backGating as potential features, the algorithm follows four major steps: (i) centering the potential features, which yields the returning value TransMatrix, (ii) using diana to compute a clustering of the potential features, (iii) cutting the tree into several clusters, and (iv) accessing outliers and rendering the final registered features with labels.

In step three, the threshold for cutting the tree is computed by

sd * thres.sigma,

where sd is the standard deviation of the distribution of the height between entities computed by diana.

A cluster is determined as an outlier if the number of its members is less than the median of the numbers of all clusters' members times 'lambda'.

Value

register

A list containing registered features for each sample.

Author(s)

Chao-Jen Wong

See Also

diana, BackGating, gpaSet.

Examples

## Not run: 
library(flowCore)
data(ITN)
wf <- workFlow(ITN)
tl <- transformList(colnames(ITN)[3:7], asinh, transformationId="asinh")
dat <- trnasformList(ITN, tl)
bg <- backGating(dat, xy=c("FSC", "SSC"), channels="CD3")

## End(Not run)

data(BackGating)
results <- flowStats:::idFeaturesByBackgating(bg=BackGating, nDim=2,
                       plot.workflow=TRUE, ask=TRUE)

RGLab/flowStats documentation built on July 20, 2023, 1:33 a.m.