Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 | 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.
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## 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")
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