convert.alias

<code class="command">convert.alias()</code> attempts to find all possible symbol-alias combinations for a given gene symbol, i.e.,
 it assumes the input ID to be either an Alias or a Symbol and performs multiple queries to find all possible
 counterparts. The input IDs are converted to title and upper case before querying and all possibilities are tested.
 There are species presets for Human and Mouse annotations.

Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but
that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function
in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the
'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes"
can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol()
attempts to determine the most likely current Gene Symbol.

Vidal Fey

convertid

Convert Gene IDs Between Each Other and Fetch Annotations from
Biomart

Henrik Edgren

convert.alias function

<dl><dt>id</dt>
<dd>(<code>character</code>). Vector of gene symbols.</dd>
<dt>species</dt>
<dd>(<code>character</code>). One of "Human" and "Mouse". Defaults to "Human".</dd>
<dt>db</dt>
<dd>(<code>AnnotationDb object</code>). Annotation package object.</dd></dl>

Arguments

<code class='command'>convert.alias()</code> attempts to find all possible symbol-alias combinations for a given gene symbol, i.e.,
 it assumes the input ID to be either an Alias or a Symbol and performs multiple queries to find all possible
 counterparts. The input IDs are converted to title and upper case before querying and all possibilities are tested.
 There are species presets for Human and Mouse annotations.

Convert Symbols to Aliases and Vice Versa. — convert.alias

<dl>

<dt>id</dt>
<dd>(<code>character</code>). Vector of gene symbols.</dd>


<dt>species</dt>
<dd>(<code>character</code>). One of "Human" and "Mouse". Defaults to "Human".</dd>


<dt>db</dt>
<dd>(<code>AnnotationDb object</code>). Annotation package object.</dd>

</dl>

convert.alias: Convert Symbols to Aliases and Vice Versa.

Description

Usage

Value

Arguments

See Also

Examples

	'SYMBOL': The official gene symbol.
	'ALIAS': All possible aliases.