find_abbr_species: Helper to find the two-letter character string of abbreviated...

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

Helper to find the two-letter character string of abbreviated species

Description

Helper to find the two-letter character string of abbreviated species

Usage

find_abbr_species(species = "human", abbr_species = NULL)

Arguments

species

Character string; the name of a species for the conveninent preparation of MSig data bases. 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 ortho_mart for the lookup of orthologs to human.

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.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.