prepString: Downloads and prepares STRING databases

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Downloads and prepares STRING databases

Description

prepString downloads and prepares the data sets of STRING interactions, accession lookups and gene name lookups.

Usage

prepString(
  species = "human",
  links_url = NULL,
  aliases_url = NULL,
  info_url = NULL,
  db_path = "~/proteoQ/dbs/string",
  filename = NULL,
  overwrite = FALSE
)

Arguments

species	Character string; the name of a species for the conveninent preparation of STRING databases. The species available for the convenience feature is in one of c("human", "mouse", "rat") with "human" being the default. The argument is not required for other species; instead, users will provide values under arguments links_url, aliases_url and info_url.
links_url	A URL to STRING interaction data. A valid web address is required for species other than c("human", "mouse", "rat"). At the NULL default and the species in one of c("human", "mouse", "rat"), the link will be determined automatically; note that users can overwrite the default interaction data by providing their own URL.
aliases_url	A URL to STRING aliases between string_protein_ids and protein accessions. A valid web address is required for species other than c("human", "mouse", "rat"). At the NULL default and the species in one of c("human", "mouse", "rat"), the link will be determined automatically; note that users can overwrite the default alias data by providing their own URL.
info_url	A URL to STRING display names between string_protein_ids and gene names. A valid web address is required for species other than c("human", "mouse", "rat"). At the NULL default and the species in one of c("human", "mouse", "rat"), the link will be determined automatically; note that users can overwrite the default info data by providing their own URL.
db_path	Character string; the local path for database(s). The default is "~/proteoQ/dbs/string".
filename	Use system default. Otherwise, the user-provided basename will be prepended with _ppi.tsv for network data and _expr.tsv for expression data.
overwrite	Logical; if TRUE, overwrite the downloaded database(s). The default is FALSE.

See Also

anal_prnString for protein-protein interaction networks.

Examples

prepString(
 # species = fly, 
 links_url = "https://stringdb-static.org/download/protein.links.full.v11.0/7227.protein.links.full.v11.0.txt.gz",
 aliases_url = "https://stringdb-static.org/download/protein.aliases.v11.0/7227.protein.aliases.v11.0.txt.gz",
 info_url = "https://stringdb-static.org/download/protein.info.v11.0/7227.protein.info.v11.0.txt.gz", 
 filename = string_dm.rds,
)

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.