TF_Activity: Inference of TF activity

In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity

Inference of TF activity

Description

Inference of TF activity

Usage

TF_Activity(
  tfs,
  GSDB,
  eset,
  DErslt,
  with_weight = TRUE,
  if_module = FALSE,
  ind = 1/5,
  useCorSign = TRUE
)

Arguments

tfs	a vector of selected tfs
GSDB	gene set database (a list of gene sets, each of which is comprised of a vector genes)
eset	expression set of gene expression data or gene expression matrix
DErslt	DEG results
with_weight	whether weighting factors (based on DEG p-values) are used to compute TF activity (default: TRUE)
if_module	whether the grouping scheme (activation or inhibition) depends on module detection algorithm (default: FALSE, no need to change)
ind	Hill coefficient parameter used in the weighting factors (default: 1/5, recommend to use 0 < ind < 1/4)
useCorSign	allow the option to use the TF gene expression correlation to flip signs (default: TRUE)

Value

a list of results: all_list: grouping scheme of all TF gene sets. all_activity: matrix of TF activity.

lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.