import.CITRUS: Importation of cell cluster profiles from a Citrus result

In tchitchek-lab/CytoCompare: Computational comparisons of cytometry profiles

Description

Imports one or several cell cluster profiles identified by the Citrus algorithm into a CLUSTER object.

Usage

import.CITRUS(file, dictionary = NULL, exclude = c("Time",
  "fileEventNumber", "Cell_length", "fileId"), bin.width = 0.05,
  minimumClusterSizePercent = 0.05, cluster.selection = NULL,
  arcsinh.transform = FALSE)

Arguments

file	a character indicating the location of the citrusClustering.Rdata file
dictionary	a two-column data.frame providing the correspondence between the original marker names (first column) and the new marker names (second column)
exclude	a vector containing the marker names to be excluded in the import procedure
bin.width	a numeric value indicating the width of the bins for the marker expression densities computations
minimumClusterSizePercent	a numeric value indicating the minimal ratio of cells per cluster to import
cluster.selection	a character vector containing the names of the clusters to import
arcsinh.transform	a logical value indicating if Citrus expression values must be arcsinh transformed

Details

Citrus is an algorithm that clusters cells using a hierarchical clustering procedure (similarly to SPADE) and then identifies the cell clusters that are significantly associated with different biological condition phenotypes (PMID:24979804).

Value

a S4 object of class CLUSTER

tchitchek-lab/CytoCompare documentation built on May 31, 2019, 7:29 a.m.