Description Usage Arguments Value
View source: R/make_expressed_net.R
Prioritize ligand-receptor interactions in a single condition
1 2 3 4 5 6 7 | make_expressed_net(
expression_data,
expressed_thresh,
receptor_ligand,
KL_method,
pseudo_count
)
|
expression_data |
expression matrix for ligand and receptor genes. 1st column "genes" (gene symbol, upper case); remaining columns: gene expression level |
expressed_thresh |
threshold above which a gene is considered expressed |
receptor_ligand |
receptor-ligand interaction database from Ramilowski JA et al, Nat. Comm. 2015. Provided with the package |
KL_method |
"product" or "min": ligand-receptor interaction score is either defined by multiplying ligand and receptor expression values or take the minimum |
pseudo_count |
a small value added to the expression matrices to avoid dividing by 0. |
KL divergence for all expressed ligand-receptor pairs, as well as ligand and receptor expression values across cell types. You may want to sort from highest to lowest to examine the top ones.
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