GetMarkerNames: Takes in an example file as input and returns all marker...

In Sconify: A toolkit for performing KNN-based statistics for flow and mass cytometry data

Description

This is a quick way to get a list of preferred marker names. This outputs a csv file containing all markers in the dataset in the name format that will be recognized by downstream functions. You manually alter this list to remove and/or categorize the said markers. The file can then be read in (stringsAsFactors = FALSE) to give you the marker list of interest. In particular, name the top of the column as "markers" if you're just altering the list. If you're doing to divide it into static and functional markers, produce two columns, naming them respectively.

Usage

GetMarkerNames(file)

Arguments

file	the fcs file of interest

Value

the list of markers of interest. This is to be written as a csv

Examples

file <- system.file("extdata", "Bendall_et_al_Cell_Sample_C_basal.fcs",
    package = "Sconify")
GetMarkerNames(file)

Sconify documentation built on Nov. 8, 2020, 6:45 p.m.