make_LRL_list: Find the regulatory relationships of all the (L2-R2)-(L1-R1)...
In Pinlyu3/LRLoop: Two-way communication between cells

Find the regulatory relationships of all the (L2-R2)-(L1-R1) pairs of interest

make_LRL_list(
  L2R2_network,
  L1R1_network,
  ligand_target_matrix_binary_ct1,
  ligand_target_matrix_binary_ct2,
  receptor_target_matrix_binary_ct1,
  receptor_target_matrix_binary_ct2
)

`L2R2_network`	Ligand-receptor network matrix with columns "from" and "to", signaling from ct2 to ct1
`L1R1_network`	Ligand-receptor network matrix with columns "from" and "to", signaling from ct1 to ct2
`ligand_target_matrix_binary_ct1`	A matrix of 0s and 1s with target genes in rows and ligands in columns, indicates whether each target gene is identified as a target of each ligand, signaling to/in ct1
`ligand_target_matrix_binary_ct2`	A matrix of 0s and 1s with target genes in rows and ligands in columns, indicates whether each target gene is identified as a target of each ligand, signaling to/in ct2
`receptor_target_matrix_binary_ct1`	A matrix of 0s and 1s with target genes in rows and receptors in columns, indicates whether each target gene is identified as a target of each receptor, signaling to/in ct1
`receptor_target_matrix_binary_ct2`	A matrix of 0s and 1s with target genes in rows and receptors in columns, indicates whether each target gene is identified as a target of each receptor, signaling to/in ct2

p_A_a_list: A list of four elements: p_A_a[[all_reg_info]]: (L2-R2)-(L1-R1) pairs and the regulatory relationships between these genes (1: TRUE; 0: FALSE). p_A_a[[L1->L2 & L2->L1]]: (L2-R2)-(L1-R1) pairs that regulate each other, identified based on ligand_target_matrix_binary_ct1 and ligand_target_matrix_binary_ct2 p_A_a[[R1->L2 & R2->L1]]: (L2-R2)-(L1-R1) pairs that regulate each other, identified based on receptor_target_matrix_binary_ct1 and receptor_target_matrix_binary_ct2 p_A_a[[L1->L2 & L2->L1 & R1->L2 & R2->L1]]: (L2-R2)-(L1-R1) pairs that regulate each other, identified based on [ligand_target_matrix_binary_ct1 & receptor_target_matrix_binary_ct1] and [ligand_target_matrix_binary_ct2 & receptor_target_matrix_binary_ct2]

Pinlyu3/LRLoop documentation built on Jan. 7, 2022, 3:04 p.m.