flowVS (version 1.4.2)

transFlowVS: Transform a flowSet by asinh transformation.

Description

This function transforms a flowSet by asinh transformation with the cofactors passed on to the function. The optimum cofactors that stabilize within-population variances in different fluorescence channels are estimated beforehand and passed to this function for data transformation.

Usage

transFlowVS(fs, channels, cofactors)

Arguments

fs

A flowSet containing a collection of flow cyometry samples.

channels

A character vector identifying the channels/dimensions to be transformed. If any entry in this vector is not present in the flowSet, the function returns with an error.

cofactors

A numeric vector. cofactors[i] is used with asinh function to transform the column with name specified by channels[i].

Value

• transFlowVS returns a new flowSet with the transformed channels.

Details

This function transforms a flowSet by asinh transformation with selected cofactors. The column with name channels[i] of every flowFrame of the input flowSet is transformed by asinh transformation with cofactors[i]. For example, let z_ij be the ith column of jth flowFrame in the input flowSet fs. Then after transformation z_ij would be converted to asinh(z_ij/cofactors[i]).

For variance stabiilzation, the optimum cofactors that stabilize within-population variances in different fluorescence channels are estimated beforehand and passed to this function for data transformation. Variance stabilizing cofactors can be estimatd by the estParamFlowVS function.

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

## ------------------------------------------------
## Example 1: Healthy data from flowVS package
## ------------------------------------------------
data(HD)
## identify optimum cofactor for CD3 and CD4 channels (from five samples)
cofactors = estParamFlowVS(HD[1:5],channels=c('CD3','CD4'))
## transform CD3 and CD4 channels in all samples
HD.VS = transFlowVS(HD, c('CD3','CD4'), cofactors)
densityplot(~CD3+CD4, HD.VS, main="Transfromed CD3 and CD4 channels in HD data")

## ------------------------------------------------
## Example 2: ITN data from flowStats package
## ------------------------------------------------
library(flowStats)
data(ITN)
# identify lymphocytes
ITN.lymphs = fsApply(ITN,lymphs, list("FS"=c(200, 600),"SS"=c(0, 400)), "FSC", "SSC",FALSE)
## identify optimum cofactor for CD3 and CD4 channels (from five samples)
cofactors = estParamFlowVS(ITN.lymphs[1:5],channels=c('CD3', 'CD4'))  
## transform CD3 and CD4 channels in all samples
ITN.VS = transFlowVS(ITN.lymphs, c('CD3','CD4'), cofactors)
densityplot(~CD3+CD4, ITN.VS, main="Transfromed CD3 and CD4 channels in ITN data")