cn_make_grn: Reconstruct CT-specific GRNs

cn_make_grnR Documentation

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 July 5, 2022, 5:06 a.m.