readSet: Read and Transform Flow Set

In ornelles/flowExtra: Helper Functions for flowCore

Description

A wrapper to read.flowSet to read a flow set.

Usage

readSet(
  path = ".",
  pattern = "\\d\\d\\d$",
  log.chan = NULL,
  alter.names = TRUE,
  name.keyword = "SAMPLE ID",
  phenoData = list(date = "$DATE", sample = "SAMPLE ID"),
  tfun = c("asinh", "log10"),
  depth = 10,
  log.cutoff = 2^depth,
  ...
)

Arguments

path	A character vector identifying the path to search for FSC files, defaults to current directory
pattern	Grep pattern to identify FSC files, defaults to "\d\d\d$"
log.chan	Character vector of channels to be log-transformed (after the "alter.names" option is applied)
alter.names	Logical value passed to read.flowSet to change "-" to "." in names, default value of TRUE
name.keyword	Character string for the FCS keyword used for names, default of "SAMPLE ID"
phenoData	List to serve as the rudiments of the phenoData built from the keywords "$DATE" and "SAMPLE ID"
tfun	Transformation function to apply to log-transformed values, either asinh (default) or log10
depth	Integer indicating bit depth (2^depth), 10 for FACSCaliber, 24 for Acurri
log.cutoff	Values greater than this cutoff force transformation if the argument log.chan is NULL, defaults to 2^depth
...	Additional arguments to read.flowSet

Details

Files in the directory specified by path that match the grep pattern specified in pattern will be read with read.flowSet. Parameter names will be adjusted if alter.names = TRUE to replace "-" with ".". A minimal amount of phenoData will be assigned from the $DATE and "SAMPLE ID" keywords.

Value

Flow Set with transformed and name-adjusted parameters.

ornelles/flowExtra documentation built on March 1, 2020, 9:33 a.m.