convert_fcs: Convert a flowFrame to data.frame
In ParkerICI/grappolo: Feature generation from single-cell data

Description Usage Arguments Details Value

This function converts a flowFrame object to an R data.frame, taking care of data transformation and compensation.

convert_fcs(
  f,
  asinh.cofactor = NULL,
  compensate = T,
  negative.values = "truncate",
  quantile.prob = 0.05
)

`f`	The `flowFrame` to convert
`asinh.cofactor`	Cofactor for `asinh` transformation. If this is `NULL` no transformation is performed
`compensate`	Wether to compensate the data using the compensation matrix embedded in the `flowFrame` (if any)
`negative.values`	How to deal with negative values in the data. If this is `NULL` negative values are left as is. Otherwise two options are possible: `truncate`: Negative values will be truncated (i.e. replaced with 0) `shift`: The data will be shifted so that only `quantile.prob` of the values for each channel will be truncated to 0. This option is useful in cases where the range of data significantly extends in the negatives, for instance due to compensation.
`quantile.prob`	Only used if `negative.value` is set to `shift`. The quantile of measurements that are going to be truncated to 0. For instance if this is 0.05, the data will be shifted so that only 5 percent of the values are negative and will be truncated to 0

The column names of the resulting data.frame will be derived from the channel descriptions (i.e. $PxS FCS keyword) when possible, and the cannel names otherwise ($PxN)

Returns a data.frame corresponding to the data in flowCore::exprs(f) after compensation and transformation

ParkerICI/grappolo documentation built on April 8, 2021, 11:03 a.m.