debarcode_fcs: Main wrapper for the debarcoder pipeline.

In ParkerICI/premessa: R package for pre-processing of flow and mass cytometry data

Main wrapper for the debarcoder pipeline.

Description

Takes all the parameters as input, does everything and writes back the FCS files

Usage

debarcode_fcs(
  fcs,
  bc.key,
  output.dir,
  output.basename,
  sep.threshold,
  mahal.dist.threshold = 30
)

Arguments

fcs	The input flowFrame
bc.key	The barcode key, as returned by read_barcode_key
output.dir	The output directory
output.basename	The basename of the output files. For each debarcoded sample, the sample label will be appended to this basename
sep.threshold	The minimum seperation between the lowest barcode channel, and the highest non-barcode channel. The data will be normalized before doing the assignments, therefore this number will typically be in [0, 1]
mahal.dist.threshold	The maximum squared Mahalanobis distance between each event and the centroid of the population that event has been assigned to. This is for further filtering the barcode assignments and it is not always necessary. Events with distance above this threshold are left unassigned. The distance is capped at 30, therefore the default value of this option corresponds to no filtering

Value

For each debarcoded sample, a new FCS file is created in the output directory. Unassigned events are written in a separate file

ParkerICI/premessa documentation built on Sept. 16, 2022, 3:06 p.m.