make_STRING_table: Ligand:receptor association scores

In VCCRI/scTalk: Single-cell talk - an R package for analysis of cell-cell communication networks from single-cell data.

Description

Generates a table of ligand:receptor association scores from the STRING database

Usage

make_STRING_table(
  ligands,
  receptors,
  species,
  dir.path = NULL,
  string.ver = NULL,
  verbose = FALSE,
  string.receptors = NULL,
  string.ligands = NULL,
  string.input.map = NULL
)

Arguments

ligands	a vector of ligands
receptors	a vector of receptors
species	species to use - either mouse (default) or human
dir.path	output directory for storing STRINGdb data. If not provided uses current working directory
string.ver	STRING version to use. Default is unspecified (NULL).
verbose	whether to print additional information about run (default: FALSE)
string.receptors	a list of receptor names that STRING recognises (if cannot map defaults)
string.ligands	a list of ligand names that STRING recegnises (if cannot map defaults)
string.input.map	named vector of STRING-compatable gene symbols with names corresponding to genes in dataset

Value

a data-frame containing ligands, receptors and STRING association scores between them.

Examples

## Not run: 
make_STRING_table(ligands, receptors, species="mouse")

## Or if STRING doesn't recognize some genes
string.input.map <- c("Ackr3")
names(string.input.map) <- c("Cxcr7")
string.receptors <- c("Cxcr7")
make_STRING_table(ligands, receptors, species="mouse", string.receptors=string.receptors, string.input.map=string.input.map)

## End(Not run)

VCCRI/scTalk documentation built on June 5, 2021, 6:35 a.m.