createApp {mnem} | R Documentation |
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
createApp(sets = seq_len(3), m = NULL, n = NULL, o = NULL, maxk = 5, parallel = NULL, path = "", dataonly = FALSE, allcrop = FALSE, multi = FALSE, ...)
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 |
app data object
Martin Pirkl
## recreate the app data object (takes very long, i.e. days) ## Not run: createApp() ## End(Not run) data(app)