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

Description Usage Arguments Value Examples

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

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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

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

tjburns08/Sconify documentation built on May 31, 2019, 8:56 a.m.