SuggestClusteringVar: SuggestClusteringVar

In zunderlab/FLOWMAP: Graph-based visualizations of high-dimensional single-cell data across time

SuggestClusteringVar

Description

SuggestClusteringVar returns a vector of user-specified length that contains suggested names of channels to be used as clustering.var in FLOWMAPR analysis. Chosen channels are determined based on analysis of the provided FCS files, as the variance is calculated within and between timepoints. The top varying markers are noted and tabulated, and the markers that consistently vary the most are selected.

Usage

SuggestClusteringVar(fcs.file.names, mode, var.annotate, var.remove, top.num)

Arguments

fcs.file.names	A vector of full file paths to the FCS files to be used
mode	FLOWMAPR mode to use in analysis based on starting input, available options include c("single", "multi", "one")
var.annotate	List mapping channel names to user-specified names to properly annotate all FCS file data
var.remove	Vector naming channels to be removed from all loaded FCS data
top.num	Numeric specifying the number of variables in the vector to be returned

Value

Vector naming channels that vary the most within and between FCS files

Examples

## Not run: fcs.file.names <- c(system.file("extdata/SingleFLOWMAP/d1.fcs", package = "FLOWMAPR"), 
system.file("extdata/SingleFLOWMAP/d2.fcs", package = "FLOWMAPR"))
## End(Not run)
## Not run: var.annotate <- ConstructVarAnnotate[1]
var.remove <- c("Channel3", "Channel4")

## Not run: SuggestClusteringVar(fcs.file.names, mode = "single", var.annotate,
var.remove, top.num = 20)
## End(Not run)

zunderlab/FLOWMAP documentation built on Sept. 7, 2024, 6:31 p.m.