getPPI: getPPI

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

getPPI

Description

getPPI

Usage

getPPI(
  x,
  ID = 1,
  taxID = "auto",
  required_score = NULL,
  network_type = "functional",
  add_nodes = 0,
  show_query_node_labels = 0,
  output = "igraph"
)

Arguments

x	an 'enrichResult“ object or a vector of proteins, e.g. 'c("PTCH1", "TP53", "BRCA1", "BRCA2")'
ID	ID or index to extract genes in the enriched term(s) if 'x' is an 'enrichResult' object
taxID	NCBI taxon identifiers (e.g. Human is 9606, see: [STRING organisms](https://string-db.org/cgi/input.pl?input_page_active_form=organisms).
required_score	threshold of significance to include a interaction, a number between 0 and 1000 (default depends on the network)
network_type	network type: functional (default), physical
add_nodes	adds a number of proteins with to the network based on their confidence score (default:1)
show_query_node_labels	when available use submitted names in the preferredName column when (0 or 1) (default:0)
output	one of 'data.frame' or 'igraph'

Details

[Getting the STRING network interactions](https://string-db.org/cgi/help.pl?sessionId=btsvnCeNrBk7).

Value

a 'data.frame' or an 'igraph' object

Author(s)

Yonghe Xia and modified by Guangchuang Yu

YuLab-SMU/clusterProfiler documentation built on Nov. 14, 2024, 3:10 a.m.