GRN {MoonlightR} | R Documentation |
This function carries out the gene regulatory network inference using parmigene
GRN(TFs, DEGsmatrix, DiffGenes = FALSE, normCounts, kNearest = 3, nGenesPerm = 10, nBoot = 10)
TFs |
a vector of genes. |
DEGsmatrix |
DEGsmatrix output from DEA such as dataDEGs |
DiffGenes |
if TRUE consider only diff.expr genes in GRN |
normCounts |
is a matrix of gene expression with genes in rows and samples in columns. |
kNearest |
the number of nearest neighbors to consider to estimate the mutual information. Must be less than the number of columns of normCounts. |
nGenesPerm |
nGenesPerm |
nBoot |
nBoot |
an adjacent matrix
dataDEGs <- DEGsmatrix dataGRN <- GRN(TFs = rownames(dataDEGs)[1:100], DEGsmatrix = dataDEGs, DiffGenes = TRUE, normCounts = dataFilt)