drivingforce.selectTGs: Select candidate TGs for network inference and TF ranking

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

Description

Select candidate TGs for network inference and TF ranking

Usage

drivingforce.selectTGs(object, groups = NULL, tglists = NULL,
  diff.method = "welch", diff.thresh = 0.01, ...)

Arguments

object	A sincera object
groups	A vector of cell groups; if NULL, use to all defined cell groups
tglists	A list containing user-provided candidate TGs for each group specified in the groups parameter
diff.method	The method used to perform the differential expression analysis
diff.thresh	The pvalue for determining differentially expressed genes

Details

Please use the tglists parameter to provide pre-selected tgs Otherwise, the function will select candidate TGs for each group using the following criteria: Genes differentially expressed in the cell group (pvalue < diff.thresh)

Value

An updated sincera object, use getDF with name="tgs" to access the selected TGs

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.