Description Usage Arguments Value Examples
View source: R/viper_wrapper.R
This function is a convenient wrapper for the
viper
function using DoRothEA regulons.
1 |
input |
An object containing a gene expression matrix with genes
(HGNC/MGI symbols) in rows and samples in columns. The object can be a
simple matrix/data frame or complexer objects such as
|
regulons |
|
options |
A list of named options to pass to
|
tidy |
Logical, whether computed tf activities scores should be returned in a tidy format. |
A matrix of normalized enrichment scores for each TF across all
samples. Of note, if you provide Bioconductor objects as input the function
will return this object with added tf activities at appropiate slots. e.g.
Seurat object with a new assay called dorothea
. For all
other inputs the function will return a matrix. If tidy
is
TRUE
the normalized enrichment scores are retured in a tidy format
(not supported for Bioconductor objects).
1 2 3 4 5 6 7 8 9 10 11 | # use example gene expression matrix from bcellViper package
library(bcellViper)
data(bcellViper, package = "bcellViper")
# acessing (human) dorothea regulons
# for mouse regulons: data(dorothea_mm, package = "dorothea")
data(dorothea_hs, package = "dorothea")
# run viper
tf_activities <- run_viper(dset, dorothea_hs,
options = list(method = "scale", minsize = 4,
eset.filter = FALSE, cores = 1,
verbose = FALSE))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.