transFlowVS {flowVS} | R Documentation |
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.
transFlowVS(fs, channels, cofactors)
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. |
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 i
th column of j
th 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.
transFlowVS
returns a new flowSet with the transformed channels.
Ariful Azad
Ariful Azad, Bartek Rajwa, and Alex Pothen (2015), "flowVS: Channel-Specific Variance Stabilization in Flow Cytometry", BMC Bioinformatics, vol 17, pp 1-14, 2016.
## ------------------------------------------------ ## 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")