createApp: Creating app data.

In cbg-ethz/mnem: Mixture Nested Effects Models

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 = "",
  types = c("data", "lods", "mnem"),
  allcrop = FALSE,
  multi = FALSE,
  file = NULL,
  ...
)

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: "path/"
types	types of data/analysis; "data" creates the gene expression matrix, "lods" includes the log odds, "mnem" additionally performes the mixture nem analysis; default c("data", "lods", "mnem")
allcrop	if TRUE, does not restrict and uses the full CROPseq dataset
multi	if TRUE, includes cells with more than one perturbed gene
file	path and filename of the rda file with the raw data from the command "data <- createApp(..., types = "data")"
...	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)

cbg-ethz/mnem documentation built on Nov. 7, 2024, 7:35 p.m.