enrich_TF_ChEA3_scExp: Find the TF that are enriched in the differential genes using...

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Find the TF that are enriched in the differential genes using ChEA3 database

Description

Find the TF that are enriched in the differential genes using ChEA3 database

Usage

enrich_TF_ChEA3_scExp(
  scExp,
  qval.th = 0.01,
  logFC.th = 1,
  min.percent = 0.01,
  peak_distance = 1000,
  use_peaks = FALSE,
  progress = NULL,
  verbose = TRUE
)

Arguments

scExp	A SingleCellExperiment object containing list of differential features.
qval.th	Adjusted p-value threshold to define differential features. (0.01)
logFC.th	Fold change threshold to define differential features. (1)
min.percent	Minimum fraction of cells having the feature active to consider it as significantly differential. (0.01)
peak_distance	Maximum distanceToTSS of feature to gene TSS to consider associated, in bp. (1000)
use_peaks	Use peak calling method (must be calculated beforehand). (FALSE)
progress	A shiny Progress instance to display progress bar.
verbose	A logical to print message or not. (TRUE)

Value

Returns a SingleCellExperiment object containing list of enriched Gene Sets for each cluster, either in depleted features, enriched features or simply differential features (both).

Examples

data("scExp")

scExp = enrich_TF_ChEA3_scExp(
 scExp,
 qval.th = 0.01,
 logFC.th = 1,
 min.percent = 0.01)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.