compile_fcs: Compile all .fcs files in a directory to a flowset

In shdam/cyCombine: Robust integration of single-cell cytometry datasets within and across technologies

Compile all .fcs files in a directory to a flowset

Description

A simple function to compile a directory of FCS files into a flowSet object using flowCore::read.flowSet(). Use the pattern argument to select only a subset of FCS files.

Usage

compile_fcs(
  data_dir,
  pattern = "\\.fcs",
  column.pattern = NULL,
  invert.pattern = FALSE
)

Arguments

data_dir	Directory containing the .fcs files
pattern	The pattern to use to find the files in the folder
column.pattern	An optional regular expression defining parameters we should keep when loading the file. The default is NULL.
invert.pattern	logical. By default, FALSE. If TRUE, inverts the regular expression specified in column.pattern. This is useful for indicating the channel names that we do not want to read. If column.pattern is set to NULL, this argument is ignored.

See Also

Other dataprep: convert_flowset(), prepare_data(), transform_asinh()

Examples

## Not run: 
fcs <- compile_fcs(data_dir = "_data/raw", pattern = "\\.fcs")

## End(Not run)

shdam/cyCombine documentation built on June 12, 2022, 11:29 p.m.