create_gene_lookup: Create gene lookup

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Create gene lookup

Description

Uses select to produce a lookup array for converting gene names If using the default value for db_object(org.Hs.eg.db) the values for the inputs and outputs include any listed in https://www.bioconductor.org/help/course-materials/2014/useR2014/Integration.html, although the most common will likely be: ENTREZID, ACCNUM, ALIAS, UNIGENE, ENSEMBL, ENSEMBLPROT, ENSEMBLTRANS, GENENAME, UNIPROT, OMIM, UCSCKG, SYMBOL

Usage

create_gene_lookup(
  input_values,
  input_type,
  output_type,
  sep = "\t",
  db_object = NULL
)

Arguments

input_values	Character vecter of names to lookup
input_type	String of the input values. See description for common options.
output_type	String of the ouput values. See description for common options.
sep	String to indicate how gene names should be collapsed. a value of NULL will return just the first item of the returned results
db_object	AnnotationDb object. If left null it will be set to org.Hs.eg.db.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_gene_lookup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Value

Named array that can be used to lookup gene values

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.