Description Usage Arguments Value
A ligand-receptor pair is considerd when both the ligand and receptor genes are enriched in one cell type (e.g., expressed 3 fold higher in cell type A than each of the other cell types) The resulting ligand-receptor network is then compared against talklr
1 | make_deg_net(expression_data, expressed_net, fc_thresh, pseudo_count)
|
expression_data |
expression matrix for ligand and receptor genes. 1st column "genes" (gene symbol, upper case); remaining columns: gene expression level |
expressed_net |
the output from calling make_expressed_net.R function. To ensure the input network to both algorithms are the same. |
fc_thresh |
fold change threshold above which a gene is considered enriched |
pseudo_count |
a small value added to the expression matrices to avoid dividing by 0. |
ligand-receptor network where both ligand and receptor genes are uniquely enriched in one cell type (i.e, marker genes for each cell type)
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