calculate_baseline: Calculate baseline for normalization

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

Calculate baseline for normalization

Description

Extract beads events from all the FCS files in the working directory and calculates the baseline for normalization

Usage

calculate_baseline(
  wd,
  beads.type,
  files.type = c("data", "beads"),
  beads.gates = NULL
)

Arguments

wd	Working directory (character)
beads.type	Type of beads. Must be on of "Fluidigm", "Beta"
files.type	The type of FCS files contained in wd. If data, the files represent full datasets (i.e. beads + cells events), the gates in beads.gates will be applied to extract the beads, and the median intensity of the beads events will be returned to be used as baseline for normalization. If beads, the files are assumed to only contain beads events. The beads.gates parameter is ignored, and the median of all the beads events (i.e. the entire content of the files) will be returned.
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

Value

Returns a vector with the medians of the beads events across all processed files

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