corsym: Correct unofficial gene symbols.

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

Description

Function to correct and unify gene identifiers across a study arms.

Usage

corsym(symbol_set, symref = NULL, verbose = T, col2 = "Chrom",
  correctionsfile = "./reference_data/gene_symbol_corrections_list.txt")

Arguments

symbol_set	the set of gene identifiers to be corrected
symref	The gene identifier lookup table containing a set of official gene symbols. If this contains two columns, it should be in the format of the hgnc.table data set provided by the CRAN package, HGNChelper. Else, this should be a whole data table of gene symbol look ups as provided by genenames.org
verbose	If set to TRUE, this flag will cause the gene symbol corrections to be conducted automatically.
col2	If two columns of data are provided as the symbol_set input to corsym, col2 should provide the name of a second column containing additional data bout the gene identifier to be checked, such as a chromosomal location.
correctionsfile	character string giving the file path to the a gene symbol corrections file. This file should contain two columns: old_symbol and new_symbol containing the errant and the correct symbols, respectively. This is the primary set of symbols to be used in coordinating gene symbol corrections between the multiple arms of the study.

Details

This function allows a user to interactively correct gene identifiers so they can be coordinated between study arms. All corrections can optionally be recorded to the corrections file so that at latter time they can be run automatically, without user interaction, and so that they can be automatically re-used in correcting gene symbols from other study arms.

Value

The character vector of gene identifiers provided as an input, with any possible corrections made.

Examples

toCheck = c("p53", "FLT3", "ASM1", "ASML3B","ARF","APOBEC3C")
corrected = corsym(symbol_set=toCheck) #using HGNChelper and previously made corrections

symref  = getHugoSymbols()

## Not run: 
symref  = getHugoSymbols(curhugofname="./reference_data/current_hugo_table_slim.txt")
corrected = corsym(symbol_set=toCheck, symref=symref, verbose=T)

## End(Not run)

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