map_to_entrez_os_name: Map uniprot or refseq to entrez (not currently used)

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

Map uniprot or refseq to entrez (not currently used)

Description

Map uniprot or refseq to entrez (not currently used)

Usage

map_to_entrez_os_name(
  species = "human",
  abbr_species = NULL,
  os_name = "Homo sapiens",
  from = "UNIPROT",
  filename = NULL,
  db_path = "~/proteoQ/dbs/entrez",
  overwrite = FALSE
)

Arguments

species	Character string; the name of a species.
abbr_species	Two-letter character string; the abbreviated name of species used with org.Xx.eg.db. The value of abbr_species will be determined automatically if the species is in one of c("human", "mouse", "rat"). Otherwise, for example, users need to provide abbr_species = Ce for fetching the org.Ce.eg.db package in the name space of proteoQ. For analysis against gene ontology and Molecular Signatures, the argument is further applied to differentiate the same biological terms under different species; e.g., GO~0072686 mitotic spindle becomes hs_GO~0072686 mitotic spindle for human and mm_GO~0072686 mitotic spindle for mouse.
os_name	An organism name by UniProt.
from	the type of keys
filename	Character string; An output file name. At the NULL default, the name will be determined automatically at a given species; i.e., msig_hs.rds for human data. The file is saved as a .rds object for uses with prnGSPA.
db_path	Character string; the local path for database(s). The default is "~/proteoQ/dbs/entrez".
overwrite	Logical; if TRUE, overwrite the downloaded database(s). The default is FALSE.

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