idFeaturesByBackgating {flowStats} | R Documentation

## (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)

[Package flowStats version 4.0.0 Index]