createApp {mnem}R Documentation

Creating app data.

Description

This function is for the reproduction of the application results in the vignette and publication. See the publication Pirkl & Beerenwinkel (2018) on how to download the data files: GSE92872_CROP-seq_Jurkat_TCR.digital_expression.csv k562_both_filt.txt GSM2396861_k562_ccycle_cbc_gbc_dict.csv GSM2396858_k562_tfs_7_cbc_gbc_dict.csv

Usage

createApp(sets = seq_len(3), m = NULL, n = NULL, o = NULL,
  maxk = 5, parallel = NULL, path = "", dataonly = FALSE,
  allcrop = FALSE, multi = FALSE, ...)

Arguments

sets

numeric vector with the data sets: 1 (CROPseq), 2, 3 (both PERTURBseq); default is all three

m

number of Sgenes (for testing)

n

number of most variable E-genes (for testing)

o

number of samples per S-gene (for testing)

maxk

maximum number of component in mnem inference (default: 5)

parallel

number of threads for parallelisation

path

path to the data files path/file.csv

dataonly

if TRUE, only fetches and normalizes the data and computes the log odds

allcrop

if TRUE, does not restrict and uses the full CROPseq dataset

multi

if TRUE, includes cells with more than one perturbed gene

...

additional parameters for the mixture nem function

Value

app data object

Author(s)

Martin Pirkl

Examples

## recreate the app data object (takes very long, i.e. days)
## Not run: 
createApp()

## End(Not run)
data(app)

[Package mnem version 1.0.0 Index]