correctByHgncHelper: Correct gene symbols using the HGNChelper package

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

Description

Correct gene symbols using the HGNChelper package. Provides interactive or automatic correction of gene identifiers, and corrdination of any correction between multiple calls to this functions.

Usage

correctByHgncHelper(symbol_set,
  correctionsfile = "./reference_data/gene_symbol_corrections_list.txt",
  symtab = NULL, verbose = F)

Arguments

symbol_set	Vector, matrix or data.frame (if more than 2 dimensions, the symbols must be in the first column)
correctionsfile	A file name for a file of gene symbol corrections. This file should be tab delimited and contain two named columns: old_symbol and new_symbol. The old_symbol column contains incorrect identifiers to be corrected, and the new_symbol column contains the corrections. There should be no row names.
symtab	The table of official, orthodox gene identifiers. If not provided, the hgnc.table data frame object from HGNChelper will be used.
verbose	A logical flag indicating if interactive mode should be run.

Value

A character vector containing the identifiers for the set of genes provided in the symbol_set function argument, but with any applicable corrections made.

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