read.FCS_comma: A modified version of flowCores read.FCS

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

A modified version of flowCores read.FCS

Description

Please see ?flowCore::read.FCS for documentation. The additional feature of this modified version is the attempt to read compensation-matrices (SPILL keyword) which have been written with a comma as decimal separator instead of a dot. This error may occurs, when the language computer of BD Flow Cytometer is set German. In this case the DIVA software writes an FCS file which does not obey the international standard of using a dot as decimal separator. FlowJo by the way ignores this problem and just read the FCS file ignoring the SPILL keyword. In this case information is lost but the file can be used for further analyses. FlowCores read.FCS function though does not read these files.

Usage

read.FCS_comma(
  filename,
  transformation = "linearize",
  which.lines = NULL,
  alter.names = FALSE,
  column.pattern = NULL,
  invert.pattern = FALSE,
  decades = 0,
  ncdf = FALSE,
  min.limit = NULL,
  truncate_max_range = TRUE,
  dataset = NULL,
  emptyValue = TRUE,
  channel_alias = NULL,
  ...
)

Arguments

filename	see ?read.FCS
transformation	see ?read.FCS
which.lines	see ?read.FCS
alter.names	see ?read.FCS
column.pattern	see ?read.FCS
invert.pattern	see ?read.FCS
decades	see ?read.FCS
ncdf	see ?read.FCS
min.limit	see ?read.FCS
truncate_max_range	see ?read.FCS
dataset	see ?read.FCS
emptyValue	see ?read.FCS
channel_alias	see ?read.FCS
...	see ?read.FCS

Details

In essence the function txt2spillmatrix tries to to guess which comma is a decimal separator and which one is a separator for different entries in the compensation matrix. One assumption is that the diagonal of the matrix has 1s only.

Value

a flowFrame with corrected SPILL keyword

Examples

## Not run: 
# read the FCS file while the spill keyword is fixed (wrong comma replaced by dots)
ff <- read.FCS_spill.comma.sensitive(filename = "123.fcs")
# save the correct version as new file or overwrite the old one
# NOTE: the meta data reveal that the file was read and saved with flowCore
flowCore::write.FCS(x = ff, filename = "123_spill_corr.fcs")

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.