SSNcompute: SSNcompute

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

SSNcompute

Description

get all PCC values of exact feature from feature-coupled network

if the element (edge) is NA, this feature couple (nodes) will be ignored

Usage

SSNcompute(
  ss_gex,
  ref_gex,
  delta_p = 0.1,
  ref_p = 0.05,
  prior_network = NULL,
  nFirstOrderNeighbor = 3,
  nSecondOrderNeighbor = 1,
  sED_scale = TRUE,
  save_dir = NULL,
  quiet = FALSE
)

Arguments

ss_gex	gene expression matrix of single sample(s)
ref_gex	gene expression matrix of reference
delta_p	p_value threshold for delta PCC test
ref_p	p_value threshold for correlation test, when building gene network from reference
prior_network	the prior network, such as experimental protein-protein interaction (PPI network) NULL (default) or a data.frame that has 2 columns of node couples
nFirstOrderNeighbor	the least number of first-order neighbor(s) for each gene, default 3
nSecondOrderNeighbor	the least number of second-order neighbor(s) for each gene, default 1
sED_scale	whether to scale sED by standard deviation
save_dir	the directort for saving SSN network data.frame, default NULL (not save)
quiet	do not print output of process during calculation (against verbose), default FALSE

Value

S4::SSN object, output will be stored in object@network

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