cal_activity: The core function to compute the activity profile of an TF

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

The core function to compute the activity profile of an TF

Description

The core function to compute the activity profile of an TF

Usage

cal_activity(
  gs_remain,
  tmp_data,
  tmp_sign,
  ind,
  with_weight,
  DE_weights,
  tf_exprs,
  useCorSign = useCorSign
)

Arguments

gs_remain	a vector of target genes after filtering
tmp_data	gene expression of target genes
tmp_sign	sign of target genes (+1 for one group, -1 for the other)
ind	Hill coefficient parameter used in the weighting factors (default: 1/5, recommend to use 0 < ind < 1/4)
with_weight	whether weighting factors (based on DEG p-values) are used to compute TF activity (default: TRUE)
DE_weights	a vector of the input for computing DE weighting factors (typically, adjusted p-values from DEG analysis)
tf_exprs	a vector of gene expression of the TF
useCorSign	allow the option to use the TF gene expression correlation to flip signs (default: TRUE)

Value

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

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