DNB: DNB

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

Description

Compute the Dynamic Network Biomarkers(DNB) model

Usage

DNB(
  data,
  meta,
  diffgenes,
  allgenes = NULL,
  meta_levels = NULL,
  high_method = c("high_cv", "top_gene"),
  high_cutoff = 0.6,
  cutree_method = c("h", "k"),
  cutree_cutoff = 0.98,
  minModule = 7,
  maxModule = 60,
  quiet = FALSE
)

Arguments

data	the gene expression matrix, which can be a single-cell RNA-seq GEM with at least three group/clusters or a matrix merging bulk GEMs from at least three different sample
meta	a data.frame with rownames as cell-id as well as one column of group infomation
diffgenes	which genes we're interested in
allgenes	the whole genes that ordered by expression, or the rownames of GEM (default)
meta_levels	the order of meta group, default ordered by decreasing if be null
high_method	the method to select genes for the first step, by either high_cv (default) or top_gene
high_cutoff	the cutoff value corresponding to the high_method, with the range between 0-1 for high_cv and 1-length(allgenes) for top_gene
cutree_method	the method to select tree(module) numbers, by either h (height, default) or k (number K)
cutree_cutoff	the cutoff value corresponding to the cutree_method, with the range between 0-1 for h and a number greater than 0 for k
minModule	the min number of genes of the module meeting requirements
maxModule	the max number of genes of the module meeting requirements
quiet	do not print output of process during calculation, default FALSE

Details

return a DNB_obj object

write score results into DNB_score_matrix.txt

write gene list from the Module of max CI score into DNB_maxModule.txt

Value

DNB_obj

Author(s)

Kaiyu Wang, in ChenLab of CAS, Shanghai, China

Examples

DNB(...)

Kaiyu-W/DNB documentation built on Jan. 1, 2022, 5:19 p.m.