drivingforce.selectTFs: Select candidate TFs for network inference and TF ranking

In xu-lab/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Select candidate TFs for network inference and TF ranking

Usage

drivingforce.selectTFs(object, groups = NULL, tflists = NULL,
  diff.method = "welch", diff.thresh = 0.05, min.expression = 5,
  pct.thresh = 0.8, ...)

Arguments

object	A sincera object
groups	A vector of cell groups; if NULL, use all defined cell groups
tflists	A list containing user-provided candidate TFs for each group specified in groups parameter
diff.method	The method used to perform the differential expression analysis
diff.thresh	The pvalue for determining differentially expressed genes
min.expression	The threshold expression value for determining expressed genes
pct.thresh	The percentage threshold for determining genes commonly expressed in a cell group

Details

Please use the tflists parameter to provide pre-selected TFs Otherwise, the function will select candidate TFs for each group using the following criteria: (1) TFs differentially expressed in the cell group (pvalue < diff.thresh); Or (2) TFs expressed greater than a certain percentage of the group cells (>min.expression in at least pct.thresh percentage of the group cells)

Value

An updated sincera object, use getDF with name="tfs" to access the selected TFs

xu-lab/SINCERA documentation built on Feb. 3, 2021, 4:19 a.m.