Package 'hmdbQuery'

Title: utilities for exploration of human metabolome database
Description: Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).
Authors: Vince Carey <[email protected]>
Maintainer: VJ Carey <[email protected]>
License: Artistic-2.0
Version: 1.25.0
Built: 2024-06-30 04:28:28 UTC
Source: https://github.com/bioc/hmdbQuery

Help Index

extract biospecimen associations

Description

extract biospecimen associations

Usage

## S4 method for signature 'HmdbEntry'
biospecimens(x)

Arguments

x

HmdbEntry instance

Value

character vector

Examples

data(hmdb1)
biospecimens(hmdb1)

extract disease associations

Description

extract disease associations

Usage

## S4 method for signature 'HmdbEntry'
diseases(x)

Arguments

x

HmdbEntry instance

Value

DataFrame

Examples

data(hmdb1)
diseases(hmdb1)

hmdb_disease: Sept 2017 extract from hmdb.ca of direct disease associations

Description

hmdb_disease: Sept 2017 extract from hmdb.ca of direct disease associations

Usage

hmdb_disease

Format

S4Vectors DataFrame

Note

This table also includes a column of metabolite name.

Source

www.hmdb.ca xml

hmdb_gene: Sept 2017 extract from hmdb.ca of direct gene associations

Description

hmdb_gene: Sept 2017 extract from hmdb.ca of direct gene associations

Usage

hmdb_gene

Format

S4Vectors DataFrame

Source

www.hmdb.ca xml

hmdb_omim: Sept 2017 extract from hmdb.ca of direct omim associations

Description

hmdb_omim: Sept 2017 extract from hmdb.ca of direct omim associations

Usage

hmdb_omim

Format

S4Vectors DataFrame

Source

www.hmdb.ca xml

hmdb_protein: Sept 2017 extract from hmdb.ca of direct protein associations

Description

hmdb_protein: Sept 2017 extract from hmdb.ca of direct protein associations

Usage

hmdb_protein

Format

S4Vectors DataFrame

Source

www.hmdb.ca xml

hmdb1: demonstration HMDB entry

Description

hmdb1: demonstration HMDB entry

Usage

hmdb1

Format

HmdbEntry instance

Source

www.hmdb.ca

Constructor for HmdbEntry instance

Description

Constructor for HmdbEntry instance

Usage

HmdbEntry(
  prefix = "http://www.hmdb.ca/metabolites/",
  id = "HMDB0000001",
  keepFull = TRUE
)

Arguments

prefix

character(1) URL of HMDB source accepting queries for XML documents
id

character(1) HMDB identifier tag
keepFull

logical(1) indicating that entire parsed XML will be retained

Value

instance of HmdbEntry, or a list

Note

The XML returned by hmdb.ca can have different structures for different metabolites. If the mapping form XML to list is not as anticipated for a given metabolite, the xmlToList result is returned with a warning. Such entries should be reported to the hmdbQuery maintainer for map revision.

Examples

HmdbEntry()

basic container for an HMDB metabolite entry

Description

basic container for an HMDB metabolite entry

Slots

metabolite

character(1) institutional name of metabolite

id

HMDB identifier

diseases

S4Vectors DataFrame instance listing associated diseases

biospecimens

S4Vectors DataFrame instance listing associated biospecimens

tissues

S4Vectors DataFrame instance listing associated tissues

store

contains parsed XML

Note

Ontological tagging of diseases and other associated elements should be considered.

extract general association metadata in store slot

Description

extract general association metadata in store slot

Usage

## S4 method for signature 'HmdbEntry'
store(x)

Arguments

x

HmdbEntry instance

Value

list

Examples

data(hmdb1)
names(store(hmdb1))

extract tissue associations

Description

extract tissue associations

Usage

## S4 method for signature 'HmdbEntry'
tissues(x)

Arguments

x

HmdbEntry instance

Value

character vector

Examples

data(hmdb1)
tissues(hmdb1)