convert_fcs: Convert a flowFrame to data.frame

Description Usage Arguments Details Value

View source: R/io.R

Description

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

Usage

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

Arguments

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

Details

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)

Value

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


ParkerICI/scfeatures documentation built on April 10, 2021, 9:31 a.m.