SplitFile: Runs "process.multiple.files" on a single file, splits it...

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

Description

This is meant to serve as a control for the basic "unstim" and "stim" pipeline that is generally used within this package. If phosphoproteins are being compared across conditions, for example, then there should be no difference in the case that you split the same file and compare the two halves.

Usage

SplitFile(file, transform = "asinh", numcells = 10000, norm = FALSE,
  scale = FALSE, input.markers)

Arguments

file	the file we're going to split
transform	if set to asinh, performs asinh transformation on all markers of the dataset
numcells	the number of total cells to be subsampled to, set at 10k for default
norm	boolean of whether data should be quantile normalized
scale	boolean of whether data should be z-scored
input.markers	vector of strings indicating the markers to be used as input

Value

tibble containing original markers and all values calculated by SCONE

Examples

file <- system.file("extdata", "Bendall_et_al_Cell_Sample_C_basal.fcs",
    package = "Sconify")
SplitFile(file, input.markers = input.markers)

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