CODEWITHSUNDEEP
rbioconductor
Natasha
Natasha

Reputation: 1521

Querying contents from a database in R

I am using hmdbquery package, in Bioconductor package of R,to filter the concentration of some of the metabolites documented in HMDB database.

I'm referring to the hmdbquery manual that is available here . I'm facing challenge in finding the appropriate command that has to be used to parse the normal concentration of the species(please refer to the image) ,HMDB0000001, given here.

library(hmdbQuery)
lk1 = HmdbEntry(prefix = "http://www.hmdb.ca/metabolites/", id = "HMDB0000001")

From, lk1 how can I access the contents pertaining to the HMDB ID: HMDB0000001 The class of lk1 is S4 . COncentration Could someone help?

Upvotes: 0

Views: 245

Answers (1)

Martin Morgan
Martin Morgan

Reputation: 46856

When I display the object I see

> lk1
HMDB metabolite metadata for 1-Methylhistidine:
There are 10 diseases annotated.
Direct association reported for 5 biospecimens and 2 tissues.
Use diseases(), biospecimens(), tissues() for more information.

So I try one of the suggestions, e.g.,

> diseases(lk1)
DataFrame with 10 rows and 4 columns
          metabolite                   disease                          pmids
         <character>               <character>                         <List>
1  1-Methylhistidine       Alzheimer's disease  9693263,10494443,15465626,...
2  1-Methylhistidine                 Pregnancy    2994907,663967,12698507,...
3  1-Methylhistidine  Diabetes mellitus type 2  15899597,15982426,6321058,...
4  1-Methylhistidine            Kidney disease 11573638,12032193,11380830,...
5  1-Methylhistidine Maple syrup urine disease  6422161,12101068,10508118,...
6  1-Methylhistidine                   Obesity 15899597,17264178,16253646,...
7  1-Methylhistidine        Propionic acidemia  19809936,19551947,2226555,...
8  1-Methylhistidine  Eosinophilic esophagitis                               
9  1-Methylhistidine        Early preeclampsia                       22494326
10 1-Methylhistidine   Late-onset preeclampsia                       23159745
     accession
   <character>
1  HMDB0000001
2  HMDB0000001
3  HMDB0000001
4  HMDB0000001
5  HMDB0000001
6  HMDB0000001
7  HMDB0000001
8  HMDB0000001
9  HMDB0000001
10 HMDB0000001

Is this what you want?

Upvotes: 1

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