normalize_folder: Normalize a folder of FCS files

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

Normalize a folder of FCS files

Description

Main wrapper for the normalization pipeline. Use beads gates to identify beads, calculate a baseline for normalization and then normalize the files, writing new output FCS

Usage

normalize_folder(wd, output.dir.name, beads.gates, beads.type, baseline = NULL)

Arguments

wd	Working directory (character)
output.dir.name	Name of the output directory (character). The output directory will be created as a subfolder of the Working directory
beads.gates	Gates to identify the beads. This is a data structure with the following format list(file_name = list(channel_name = list(x = [xMin, xMax], y = [yMin, yMax]), ...), ...). Note that only files in names(beads.gates) will be processed. Also note that the data structure may contain gates for extra channels, but which channels will be used depends on the beads.type parameter
beads.type	Type of beads. Must be on of "Fluidigm", "Beta"
baseline	If NULL the median beads intensities of the current files will be used as baseline for normalization. Alternatively this can be a character string with the path of a directory containing FCS files of beads events, whose median intensities will be used as baseline.

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