map_identifiers: Documentation

In icb-knowing/biomapr: ID Mapping for Biology

Description

Matches one or a group of given identifiers of gene, protein, transcript or gene symbol with unknown identifiers according to given filters.

Usage

mapIdentifiers(source_ids, source_bioelement, source_datasource, 
target_bioelement, target_datasource)

Arguments

source_ids	a single identifier or a character vector of identifiers. If some of the provided identifiers don't exist, they will be ignored.
source_bioelement	character string: the type of source element. Possible values are "gene", "protein", "transcript" and "genesymbol".
source_datasource	character string: source database name. Possible values are "ncbigene", "ensembl", "uniprot", "refseq", or "-". The value of "-" corresponds to any database currently known. See Examples for the details.
target_bioelement	character string: the type of target elements. Possible values are "gene", "protein", "transcript" and "genesymbol".
target_datasource	character string: target database name. Possible values are "ncbigene", "ensembl", "uniprot", "refseq", or "-". The value of "-" corresponds to all databases currently known. See Examples for the details.

Details

Returns all mappings with a distance of 1 to 3 for a given (set of) input identifiers (source_ids) to identifiers of a given type: the target_bioelement (gene/protein/transcript/genesymbol).

Mapping is done within the range of distances:

• distance 1 – there is a direct mapping path between source_bioelement and target_bioelement;

• distance 2 – there is one or multiple mapping paths between source_bioelement and target_bioelement through one intermediate step, e.g. a gene connected to a protein through a transcript;

• distance 3 – currently the max distance for elements to be mapped. If the distance exceeds 3, the elements won't be mapped.

Within this range the function finds and returns the min distance number and all corresponding shortest paths descriptions between two elements.

IMPORTANT for NCBI ids: Please make sure you convert the identifier properly from factor/numeric to character before passing it to the mapIdentifiers() function.

Value

An object of class "data.frame" with folowing columns will be returned:

• source_id – given source identifier;

• source_bioelement – given source bioelement;

• source_datasource – the database name of the given identifier;

• target_id – found target identifier;

• target_bioelement – found target bioelement matching the given target bioelement;

• target_datasource – the database name of the found identifier;

• distance – the length of the shortest path between the source and the target identifiers;

• paths – all shortest paths found between the source and the target identifiers. The example of the path: (Gene ncbigene, 26)-[MAPS ensembl]-(Gene ensembl, ENSG00000002726)-[CODES ensembl]-(Transcript ensembl, ENST00000416793)

The data.frame contains as many rows as many matching target ids are found.

An empty data.frame is returned if no mappings up to distance 3 to the target bioelement exist.

If some of the provided source ids don't exist, they are ignored. No error or warning is returned for these ids.

Examples

### Mapping gene with the identifier "26" from any known database 
### to all related transcripts from all databases currently known.

mapIdentifiers("26","gene","-","transcript","-")


### Same query, but specifying the source database. 
### Mapping gene with the identifier "26" from NCBI gene to all 
### related transcripts from all databases currently known.

mapIdentifiers("26","gene","ncbigene","transcript","-")


### Same query, but specifying the target database. 
### Mapping gene with the identifier "26" from NCBI gene to all 
### related transcripts from RefSeq.

mapIdentifiers("26","gene","ncbigene","transcript","refseq")


### Map the gene symbol "TNF" to Ensembl genes

mapIdentifiers("TNF","genesymbol","-","gene","ensembl")


### Map the NCBI gene id "7124" to Uniprot proteins

mapIdentifiers("7124","gene","ncbigene","protein","uniprot")


### Map a list of NCBI gene ids to proteins
### from all databases currently known.

mapIdentifiers(c("26","81539"),"gene","ncbigene","protein","-")

icb-knowing/biomapr documentation built on May 25, 2019, 6:22 p.m.