read.SCsignalR: Read output from SingleCellSignalR

In martaint/InterCellar: InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Read output from SingleCellSignalR

Description

SCSR description: the output folder is a collection of txt files, one for each clusters pair considered. The "paracrine" option looks for ligands expressed in cluster A and their associated receptors according to LRdb that are expressed in any other cluster but A. These interactions are labelled "paracrine". The interactions that involve a ligand and a receptor, both differentially expressed in their respective cell clusters according to the **edgeR** analysis performed by the **cluster_analysis()** function, are labelled "specific". The "autocrine" option searches for ligands expressed in cell cluster A and their associated receptors also expressed in A. These interactions are labelled "autocrine". Additionally, it searches for those associated receptors in the other cell clusters (not A) to cover the part of the signaling that is "autocrine" and "paracrine" simultaneously. These interactions are labelled "autocrine/paracrine". This file is a 4-column table: ligands, receptors, interaction types ("paracrine", "autocrine", "autocrine/paracrine" and "specific"), and the associated LRscore. InterCellar: rename autocrine|paracrine to paracrine

Usage

read.SCsignalR(folder)

Arguments

folder

containing output from SingleCellSignalR, named cell-signaling

Value

input.data: preprocessed object with annotated L-R pairs

martaint/InterCellar documentation built on April 7, 2022, 11:44 a.m.