lymphs: Identify lymphocyte cells from a flow cytometry sample.

In flowVS: Variance stabilization in flow cytometry (and microarrays)

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.

Details

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

Value

lymphs returns a new flowFrame containing the lymphocytes.

Author(s)

Ariful Azad

References

Ariful Azad, Bartek Rajwa, and Alex Pothen (2015), "flowVS: Channel-Specific Variance Stabilization in Flow Cytometry", BMC Bioinformatics, vol 17, pp 1-14, 2016.

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)

flowVS documentation built on April 7, 2021, 6 p.m.