getHugoSymbols: getHugoSymbols

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

obtains HGNC/HUGO symbol look up table containing official set of HUGO symbols.

Usage

getHugoSymbols(paths_detail = NULL, curhugofname = NULL, verbose = F)

Arguments

paths_detail	A Path_Detail or a Study object. If a Path_Detail object is provided, the symbols will be extracted from its symtable slot. If a Study object is provided for this argument, the symbol lookup table will be exracted from the Path_Detail it contains.
curhugofname	If interactive gene symbol correction is to be used, this argument should be the file path to the HUGO table as downloaded from genenames.org.
verbose	Controlls if symbol corrections are to be interactive (if yes, curhugofname file must be supplied as it contains critical information, such as gene symbol status, past identifiers and synonyms)

Value

Table of symbols: either a two column data.frame, the hgnc.table provided by HGNChelper, or a data frame as provided by genenames.org. Either of which have a column titled Approved.Symbol which contains official, approved symbols.

Examples

#get the default HUGO lookup table, hgnc.table from HGNChelper.
hsyms = getHugoSymbols() 
#attempt to download and or use a full hugo lookup table from genenames.org
hsyms = getHugoSymbols(curhugofname="./reference_data/current_hugo_table_slim.txt") 

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.