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 = "",
      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)

[Package mnem version 1.8.0 Index]