README.md

In seandavi/MungeCuratedMGS: Data munging for Curated Microbiome Signatures

Data model slides

Link

Installation

```{r eval=FALSE} BiocManager::install('seandavi/MungeCuratedMGS')

```{r message=FALSE, warning=FALSE}
library(MungeCuratedMGS)

Data entities

See working document for details of where we are headed.

Signatures

Before running this vignette

```{r eval=FALSE} library(googlesheets) token = gs_auth() saveRDS(token, file = "/tmp/googlesheets_token.rds")

```{r sig_table_from_gs}
library(googlesheets)
suppressMessages(gs_auth(token = "/tmp/googlesheets_token.rds", verbose = FALSE))
sig_table = create_signatures_table()
head(sig_table)

Ontologies

EFO

```{r efo} efo = get_efo() head(efo)

### UBERON

```{r uberon}
uberon = get_uberon()
head(uberon)

Ontologies can be combined like so:

library(dplyr)
full_ontologies = dplyr::bind_rows(uberon, efo)

NCBI Taxonomy

Names and Taxon IDs

```{r taxon_names} taxon_dir = get_taxon_dump_files() taxon_id_names = get_taxon_names(taxon_dir) head(taxon_id_names, 10)

### Synonyms

```{r synonyms}
synonyms_dir = get_synonyms_file()
synonyms = get_synonyms(synonyms_dir)
head(synonyms, 10)

seandavi/MungeCuratedMGS documentation built on July 17, 2021, 7:17 p.m.