cn_make_grn: Reconstruct CT-specific GRNs

In pcahan1/CellNet: Assess and improve cell fate engineering with network biology

Reconstruct CT-specific GRNs

Description

runs getRawGRN, findSpecGenes, and specGRNs

Usage

cn_make_grn(sampTab, expDat, species = "Mm", tfs = NA,
  grnSampSize = 0, normDat = FALSE, corrs = NA, zscores = NA,
  cval = 0.5, cvalGK = 0.75, dLevel = "description1",
  dLevelGK = "description6", zThresh = 4, holmSpec = 1e-06,
  prune = FALSE)

Arguments

expDat	properly normalized expression matrix
tfs	vector of transcription factors
grnSampSize	min number of samples per ct or group
normDat	whether to quantile normalize the data prior to computing correlations
corrs	matrix of gene-gene pearson correlations
zscores	CLR-defined context dependent zscores
cval	template matching threshold for overall CT specific expression
cvalGK	template matching threshold for developmentally shared CT specific expression
dLevel	column name in sample table to group samples by
holmSpec	pvalue threshold for template matching
samptTab	sample table
zthresh	GRN zscore threshold at which to remove weak edges

Value

list of overallGRN (desc), specGenes (desc), ctGRNs (desc)

Examples

system.time(grnAll<-cn_make_grn(stAll, expAll, species='Mm', zThresh=6) )

pcahan1/CellNet documentation built on May 18, 2023, 4:58 p.m.