Description Usage Arguments Value
View source: R/make_expressed_net_specify_expressed_genes.R
Instead of using an expression threshold, this function identifies interesting ligand-receptor pairs among a specific list of expressed genes provided by the user. Run this function separately for perturbed and baseline conditions before running disease_vs_normal_KL.R, so that ligand and receptor matrices are in the same order.
1 2 3 4 5 6 | make_expressed_net_specify_expressed_genes(
expression_data,
expressed_genes,
receptor_ligand,
KL_method
)
|
expression_data |
expression matrix for ligand and receptor genes. 1st column "genes" (gene symbol, upper case); remaining columns: gene expression level |
expressed_genes |
a character vector of expressed genes |
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 |
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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