gate {prada}R Documentation

Functions to gate cytometry data

Description

These functions allow the user to select a number of observations in multivariate data by circling them in two-dimensional projections of the data. gate.cytoSet calls gate.cytoFrame seperately on each frame in the set. gate.matrix does the same as gate.cytoSet but only requires a data matrix.

Usage

my.gate <- gate.cytoFrame(object, gate.colour = "red",
                          use.smoothScatter = FALSE,
                          data.min = 0, data.max = 1023,
                          max.observations = 20000)

Arguments

object cytoFrame, cytoSet or matrix of cytometry data, from which observations are to be selected by gating
gate.colour colour of the drawn polygons
use.smoothScatter logical, should the function smoothScatter be employed for plotting the data (plots data densities rather than individual points)
data.min minimum value to (theoretically occur in the data; e.g. with 10-channel-digitized data, it is 0
data.max minimum value to (theoretically occur in the data; e.g. with 10-channel-digitized data, it is 1023
max.observations maximum number of observations from the data to be plotted; large values decrease performance

Details

The user is prompted to select the two dimensions for the projection and the defines a polygon by left-mouse clicks on its vertices. To finish drawing the polygon, press the right mouse button. Observations within the polygon are computed and marked. The user is then prompted if he wants to

Value

For gate.cytoFrame and gate.matrix, it is a logical vector stating for each observation in the data (in same order) wether it was included in the defined gate (TRUE) or not (FALSE). For gate.cytoSet, it is a list of logical vectors, one for each cytoFrame in the cytoSet. The class of the result depends on the called function and is cytoFrameGate,cytoSetGate, or matrixGate.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

Classes cytoFrame-class, cytoSet-class, plot.cytoFrameGate for plotting

Examples

  ## Not run: 
    # don't run during package test, because requires user input

    # read in FCS files:
    mySet   <- readCytoSet(...)

    # let user do gating:
    mySGate <- gate.cytoSet(mySet)

    # visualize gating:
    plot(mySGate,mySet,pch=".",cex=2)
  ## End(Not run)

[Package prada version 1.6.3 Index]