cn_make_grn | R Documentation |
runs getRawGRN, findSpecGenes, and specGRNs
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)
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 |
list of overallGRN (desc), specGenes (desc), ctGRNs (desc)
system.time(grnAll<-cn_make_grn(stAll, expAll, species='Mm', zThresh=6) )
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