FindLR: Finding ligand-receptor pairs

In Coolgenome/iTALK: Characterize and Illustrate Intercellular Communication

Description

This function loads the highly expressed genes or differentail expressed genes as a dataframe. Significant interactions are found through mapping these genes to our ligand-receptor database.

Usage

FindLR(data_1, data_2 = NULL, datatype, comm_type, database = NULL)

Arguments

data_1	Data used to find the ligand-receptor pairs
data_2	Second dataset used to find ligand-receptor pairs. If set NULL, paris will be found within data_1. Otherwise, pairs will be found between data_1 and data_2. Default is NULL.
datatype	Type of data used as input. Options are "mean count" and "DEG"
comm_type	Communication type. Available options are "cytokine", "checkpoint", "growth factor", "other"
database	Database used to find ligand-receptor pairs. If set NULL, the build-in database will be used.

Value

A dataframe of the significant interactions

References

Cytokines, Inflammation and Pain. Zhang et al,2007.

Cytokines, Chemokines and Their Receptors. Cameron et al, 2000-2013

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Auslander et al, 2018.

A draft network of ligand-receptor-mediated multicellular signalling in human, Jordan A. Ramilowski, Nature Communications, 2015

Coolgenome/iTALK documentation built on Aug. 3, 2019, 3:12 p.m.