DNBcompute_custom: DNBcompute_custom

In Kaiyu-W/DNBr: Compute the Dynamic Network Biomarkers (DNB) model

DNBcompute_custom

Description

Compute the Dynamic Network Biomarkers(DNB) model with customized Modules

Usage

DNBcompute_custom(
  data,
  module_list,
  meta = NULL,
  meta_levels = NULL,
  force_allgene = TRUE,
  size_effect = TRUE,
  quiet = FALSE,
  ...
)

Arguments

data	input data, S4:DNB_output or gene expression matrix
module_list	a customized list of module gene
meta	a data.frame with rownames as cell-id as well as one column of group infomation, use if data is gene expression matrix
meta_levels	the order of meta group, default ordered by decreasing if NULL, use if data is gene expression matrix
force_allgene	whether force to use all genes from data, default TRUE
size_effect	whether consider the effect of sample size when compute CI of DNB, default TRUE
quiet	do not message
...	for future use

Details

input data from existing DNB_output object, or new data and meta

input customized modules from a list of gene set(s)

return a S3 object includes several S4 objects

Value

S3:DNB_output

Author(s)

Kaiyu Wang, in ChenLab of CAS, Shanghai, China

Examples

data(data.example)
data(meta.example)
data(module_list.example)
b <- DNBcompute_custom(data.example, module_list.example, meta.example)
b
DNBplot(b, group = "USER_CUSTOMIZED", ranking = 1, show = TRUE, save_pdf = FALSE)
DNBplot(b, group = "USER_CUSTOMIZED", ranking = 1, show = TRUE, save_pdf = FALSE)

Kaiyu-W/DNBr documentation built on April 27, 2024, 10:09 a.m.