flowVS (version 1.4.2)

lymphs: Identify lymphocyte cells from a flow cytometry sample.

Description

Identify and retain lymphocytes from a flow cytometry sample based on the forward and side scatters.

Usage

lymphs(ff, lymph.boundary, fsc, ssc, plot=FALSE)

Arguments

ff

A flowFrame containing a flow cyometry sample.

lymph.boundary

A list denoting an approximate rectangular boundary for lymphocytes. The first element of the list represents the lower and upper limit of forward scatter (FSC), and the 2nd element represents the lower and upper limit of side scatter (SSC). Example: list("FSC"=c(180000, 500000),"SSC"=c(0, 180000)).

fsc

name (or numeric index) of the forward scatter channel.

ssc

name (or numeric index) of the side scatter channel.

plot

true/false. If true then plots the rectangular and elliptical gates for the lymphocytes.

Value

• lymphs returns a new flowFrame containing the lymphocytes.

Details

At first a rectangular gate is created based on the lymph.boundary. Then the norm2Filter function is used to identify lymphocytes.

References

Ariful Azad, Bartek Rajwa, and Alex Pothen (2015), "flowVS: Channel-Specific Variance Stabilization in Flow Cytometry", manuscript submitted for publication.

See Also

estParamFlowVS

Examples

library(flowStats)
data(ITN)
# identify lymphocytes
ITN.lymphs = lymphs(ITN[[1]], list("FS"=c(200, 600),"SS"=c(0, 400)), "FSC", "SSC",TRUE)