estParamFlowVS {flowVS} | R Documentation

## Estimate optimum parameters for per-channel within-population variance stabilization.

### Description

This function estimates the variance stabilizing cofactors, one for each channel for the entire dataset. When a fluorescence channel `z` is transformed by asinh transformation with the optimum cofactor for `z`, the within-population variances of populations from all samples in the channel `z` are approximately stabilized.

### Usage

      estParamFlowVS(fs, channels)

### 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.

### Details

Let `z` be a fluorescence channel (column of a flowFrame). We consider transforming `z` by asinh transformation such that after transformation we obtain the tranformed channel asinh(`z/c`), where `c` is a normalizing cofactor.

The `estParamFlowVS` function estimates cofactors, one for each channel for the entire dataset such that the within-population variance is stabilized in each fluorescence channel. When a fluorescence channel `z` is transformed by asinh transformation with the optimum cofactor for `z`, the within-population variances of populations from all samples in the channel `z` are approximately stabilized.

### Value

`estParamFlowVS` returns a numeric vector representing the optimum cofactors for the requested channels. The optimum cofactor for the input `channels[i]` is stored in the `i`th entry of the returned vector.

### 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

`transFlowVS`

### Examples

    data(HD)
    ## identify optimum cofactor for CD3 and CD4 channels (from five samples)

    cofactors = estParamFlowVS(HD[1:5],channels=c('CD3','CD4'))
    # See detail examples in the documentation of the transFlowVS function.

[Package flowVS version 1.24.0 Index]