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Merge pull request #116 from ncats/NameChanges_Vignette
Updated function names and parameter names.
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@@ -26,7 +26,7 @@ editor_options: | |
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This vignette will provide basic steps for interacting with [RaMP-DB](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876005/) (Relational database of Metabolomic Pathways). | ||
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Details on RaMP-DB installation are also avaialble through GitHub (https://github.com/RAMP-project/RAMP). | ||
Details on RaMP-DB installation are also avaialble through GitHub (https://github.com/ncats/RaMP-DB/). | ||
Questions can be asked through the Issues tab or by sending an email to [NCATSRaMP\@nih.gov](mailto:[email protected]). | ||
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RaMP-DB supports queries and enrichment analyses. | ||
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@@ -239,7 +239,7 @@ This function takes in a vector of metabolites as an input and returns a vector | |
```{r} | ||
analytes.of.interest <- c("chebi:15422", "hmdb:HMDB0000064", | ||
"hmdb:HMDB0000148", "wikidata:Q426660") | ||
new.ontologies <- getOntoFromMeta(analytes = analytes.of.interest, db=rampDB) | ||
new.ontologies <- getOntoFromMeta(mets = analytes.of.interest, db=rampDB) | ||
datatable(new.ontologies) | ||
``` | ||
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@@ -333,11 +333,11 @@ Users can retrieve chemical classes and chemical property information from input | |
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### Retrieve Chemical Classes from Input Metabolites | ||
RaMP incorporates Classyfire and lipidMAPS classes. | ||
The function chemicalClassSurvey() function takes as input a vector of metabolites and outputs the classes associated with each metabolite input. | ||
The function getChemClass() function takes as input a vector of metabolites and outputs the classes associated with each metabolite input. | ||
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```{r} | ||
metabolites.of.interest = c("pubchem:64969", "chebi:16958", "chemspider:20549", "kegg:C05598", "chemspider:388809", "pubchem:53861142", "hmdb:HMDB0001138", "hmdb:HMDB0029412") | ||
chemical.classes <- chemicalClassSurvey(mets = metabolites.of.interest, db=rampDB) | ||
chemical.classes <- getChemClass(mets = metabolites.of.interest, db=rampDB) | ||
metabolite.classes <- as.data.frame(chemical.classes$met_classes) | ||
datatable(metabolite.classes) | ||
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@@ -369,7 +369,7 @@ classy_fire_classes <- chemical.enrichment$ClassyFire_class | |
datatable(classy_fire_classes) | ||
``` | ||
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*Note*: To explicitly view the results of mapping input IDs to RaMP, users can run the chemicalClassSurvey() function as noted in above in the section "Retrieve Chemical Class from Input Metabolites". | ||
*Note*: To explicitly view the results of mapping input IDs to RaMP, users can run the getChemClass() function as noted in above in the section "Retrieve Chemical Class from Input Metabolites". | ||
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## Connect to Different Versions of RaMP | ||
Users are able to download previous versions of RaMP, and can input queries in these earlier versions. Some annotations have been added or changed since updated versions have been posted. | ||
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