Package 'bugsigdbr'

Title: R-side access to published microbial signatures from BugSigDB
Description: The bugsigdbr package implements convenient access to bugsigdb.org from within R/Bioconductor. The goal of the package is to facilitate import of BugSigDB data into R/Bioconductor, provide utilities for extracting microbe signatures, and enable export of the extracted signatures to plain text files in standard file formats such as GMT.
Authors: Ludwig Geistlinger [aut, cre], Jennifer Wokaty [aut], Levi Waldron [aut]
Maintainer: Ludwig Geistlinger <[email protected]>
License: GPL-3
Version: 1.11.0
Built: 2024-06-30 02:56:51 UTC
Source: https://github.com/bioc/bugsigdbr

Help Index

Displaying BugSigDB signatures pages in a web browser

Description

Functionality for programmatically displaying microbe signatures on BugSigDB signature pages.

Usage

browseSignature(sname)

Arguments

sname

character. Signature name. Expected to start with a prefix of the form "bsdb:<X>/<Y>/<Z>_" encoding the corresponding BugSigDB signature ID.

Value

The URL of the selected BugSigDB signature page. If interactive, opens the URL in the default web browser.

References

BugSigDB: https://bugsigdb.org

Examples

sname <- "bsdb:215/1/1_eczema:infant-with-eczema_vs_healthy-control_UP"
  browseSignature(sname)

Displaying BugSigDB taxon pages in a web browser

Description

Functionality for programmatically displaying BugSigDB taxon pages.

Usage

browseTaxon(tax.id)

Arguments

tax.id

character. NCBI taxonomy ID.

Value

The URL of the selected BugSigDB taxon page. If interactive, opens the URL in the default web browser.

References

BugSigDB: https://bugsigdb.org

Examples

# BugSigDB taxon page for Escherichia coli
  browseTaxon("562")

Extract specific taxonomic levels from a microbe signature

Description

Functionality for extracting specific taxonomic levels (such as genus and species) from a microbe signature containing taxonomic clades in MetaPhlAn format.

Usage

extractTaxLevel(
  sig,
  tax.id.type = c("metaphlan", "taxname"),
  tax.level = "mixed",
  exact.tax.level = TRUE
)

Arguments

sig

character. Microbe signature containing taxonomic clades in MetaPhlAn format.
tax.id.type

Character. Taxonomic ID type of the returned microbe sets. Either "metaphlan" (default) or "taxname".
tax.level

character. Either "mixed" or any subset of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain"). This full vector is equivalent to "mixed".
exact.tax.level

logical. Should only the exact taxonomic level specified by tax.level be returned? Defaults to TRUE. If FALSE, a more general tax.level is extracted for microbes given at a more specific taxonomic level.

Value

a character vector storing taxonomic clades restricted to chosen taxonomic level(s).

References

BugSigDB: https://bugsigdb.org

Examples

ord <- "k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales"
 sig <- c("f__Lactobacillaceae|g__Lactobacillus",
          "f__Aerococcaceae|g__Abiotrophia|s__Abiotrophia defectiva",
          "f__Lactobacillaceae|g__Limosilactobacillus|s__Limosilactobacillus mucosae")
 sig <- paste(ord, sig, sep = "|")
 sig <- extractTaxLevel(sig, tax.level = "genus")
 sig <- extractTaxLevel(sig, tax.level = "genus", exact.tax.level = FALSE)
 sig <- extractTaxLevel(sig,
                        tax.id.type = "taxname",
                        tax.level = "genus",
                        exact.tax.level = FALSE)

Obtain meta-signatures for a column of interest

Description

Functionality for obtaining meta-signatures for a column of interest

Usage

getMetaSignatures(
  df,
  column,
  direction = c("BOTH", "UP", "DOWN"),
  min.studies = 2,
  min.taxa = 5,
  comb.fun = sum,
  ...
)

Arguments

df

data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
column

character. Column of interest. Need to be a valid column name of df.
direction

character. Indicates direction of abundance change for signatures to be included in the computation of meta-signatures. Use "UP" to restrict computation to signatures with increased abundance in the exposed group. Use "DOWN" to restrict to signatures with decreased abundance in the exposed group. Defaults to "BOTH" which will not filter signatures by direction of abundance change.
min.studies

integer. Minimum number of studies for a category in column to be included. Defaults to 2, which will then only compute meta-signatures for categories investigated by at least two studies.
min.taxa

integer. Minimum size for meta-signatures. Defaults to 5, which will then only include meta-signatures containing at least 5 taxa.
comb.fun

function. Function for combining sample size of the exposed group and sample size of the unexposed group into an overall study sample size. Defaults to sum which will simply add sample sizes of exposed and unexposed group.
...

additionals argument passed on to getSignatures.

Value

A list of meta-signatures, each meta-signature being a named numeric vector. Names are the taxa of the meta-signature, numeric values correspond to sample size weights associated with each taxon.

See Also

getSignatures

Examples

df <- importBugSigDB()

 # Body-site specific meta-signatures composed from signatures reported as both 
 # increased or decreased across all conditions of study:
 bs.meta.sigs <- getMetaSignatures(df, column = "Body site")

 # Condition-specific meta-signatures from fecal samples, increased
 # in conditions of study. Use taxonomic names instead of the default NCBI IDs:
 df.feces <- df[df$`Body site` == "Feces", ]
 cond.meta.sigs <- getMetaSignatures(df.feces, column = "Condition", 
                                     direction = "UP", tax.id.type = "taxname")

 # Inspect the results
 names(cond.meta.sigs)
 cond.meta.sigs["Bipolar disorder"]

Obtain the EFO and UBERON ontology

Description

Lightweight wrapper around ontologyIndex::get_ontology to parse the Experimental Factor Ontology (EFO) or the Uber-anatomy ontology (UBERON) from OBO format into an R object.

Usage

getOntology(onto = c("efo", "uberon"), cache = TRUE)

Arguments

onto

character. Ontology to obtain. Should be either "efo" (default) to obtain the Experimental Factor Ontology (EFO) or "uberon" to obtain the Uber-anatomy ontology (UBERON).
cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Value

An object of class ontology_index as defined in the ontologyIndex package.

References

EFO: https://www.ebi.ac.uk/ols/ontologies/efo

UBERON: https://www.ebi.ac.uk/ols/ontologies/uberon

See Also

get_ontology from the ontologyIndex package.

Examples

uberon <- getOntology("uberon")

Obtain microbe signatures from BugSigDB

Description

Functionality for obtaining microbe signatures from BugSigDB

Usage

getSignatures(
  df,
  tax.id.type = c("ncbi", "metaphlan", "taxname"),
  tax.level = "mixed",
  exact.tax.level = TRUE,
  min.size = 1
)

Arguments

df

data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
tax.id.type

Character. Taxonomic ID type of the returned microbe sets. Either "ncbi" (default), "metaphlan", or "taxname".
tax.level

character. Either "mixed" or any subset of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain"). This full vector is equivalent to "mixed".
exact.tax.level

logical. Should only the exact taxonomic level specified by tax.level be returned? Defaults to TRUE. If FALSE, a more general tax.level is extracted for microbes given at a more specific taxonomic level.
min.size

integer. Minimum signature size. Defaults to 1, which will filter out empty signature. Use min.size = 0 to keep empty signatures.

Value

a list of microbe signatures. Each signature is a character vector of taxonomic IDs depending on the chosen tax.id.type.

References

BugSigDB: https://bugsigdb.org

See Also

importBugSigDB

Examples

df <- importBugSigDB()
 sigs <- getSignatures(df)

Obtain published microbial signatures from bugsigdb.org

Description

Obtain published microbial signatures from bugsigdb.org

Usage

importBugSigDB(version = "10.5281/zenodo.10627578", cache = TRUE)

Arguments

version

character. A Zenodo DOI, git commit hash, or "devel". Defaults to the most recent stable release on Zenodo, which includes complete and reviewed content from BugSigDB. See details.
cache

logical. Should a locally cached version used if available? Defaults to TRUE.

Details

There are three different options to obtain data from BugSigDB, as determined by the version argument.

  • a Zenodo DOI: use this option if you would like to obtain one of the stable release versions of BugSigDB on Zenodo. These stable release versions of BugSigDB have been automatically checked and manually reviewed and provide for the highest data quality. Select this option if you would like to incorporate BugSigDB into analysis and published research. If not specified otherwise, the importBugSigDB function will obtain the most recent stable release from Zenodo by default.

  • "devel": use this option to obtain the latest version ("bleeding edge") of BugSigDB from the BugSigDBExports GitHub repo (see references). Note that this will also include incomplete and not reviewed content, which should be filtered out prior to an analysis. Select this option if you are a curator that actively contributes to BugSigDB and would like to access data that you and other curators have recently contributed to BugSigDB and that has not been included in a stable release yet.

  • a git commit hash: it might be occasionally of interest to obtain a specific snapshot of the BugSigDBExports GitHub repo, e.g. for the sake of debugging and troubleshooting. This can be done by providing the short 7-character git commit hash (SHA) or the full SHA of the export of choice. To provide the full SHA, go to the BugSigDBExports commits page (see references) and use the copy symbol to the left of the 7-character codes to copy the full SHA code of the export version you want to use.

Value

a data.frame.

References

BugSigDB: https://bugsigdb.org

Stable release: https://doi.org/10.5281/zenodo.10627578

Latest version (incl. not reviewed content): https://github.com/waldronlab/BugSigDBExports

Release v1.2.0: https://zenodo.org/records/10407666

Release v1.1.0: https://zenodo.org/records/6468009

Release v1.0.2: https://zenodo.org/records/5904281

Release v1.0.1: https://zenodo.org/records/5819260

Release v1.0.0: https://zenodo.org/records/5606166

BugSigDBExports commits page: https://github.com/waldronlab/BugSigDBExports/commits/devel

Examples

df <- importBugSigDB()

Restrict microbe signatures to specific taxonomic levels

Description

Functionality for restricting microbe signatures to specific taxonomic levels such as genus and species.

Usage

restrictTaxLevel(df, tax.level = "mixed", exact.tax.level = TRUE, min.size = 1)

Arguments

df

data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
tax.level

character. Either "mixed" or any subset of c("kingdom", "phylum", "class", "order", "family", "genus", "species", "strain"). This full vector is equivalent to "mixed".
exact.tax.level

logical. Should only the exact taxonomic level specified by tax.level be returned? Defaults to TRUE. If FALSE, a more general tax.level is extracted for microbes given at a more specific taxonomic level.
min.size

integer. Minimum signature size. Defaults to 1, which will filter out empty signatures. Use min.size = 0 to keep empty signatures.

Value

a data.frame with microbe signature columns restricted to chosen taxonomic level(s).

References

BugSigDB: https://bugsigdb.org

See Also

importBugSigDB

Examples

df <- importBugSigDB()
 df <- restrictTaxLevel(df, tax.level = "genus")

Ontology-based subsetting of BugSigDB signatures

Description

This function facilitates ontology-based queries for experimental factors and body sites.

Usage

subsetByOntology(df, column = c("Body site", "Condition"), term, ontology)

Arguments

df

data.frame storing BugSigDB data. Typically obtained via importBugSigDB.
column

character. Column of df on which subsetting should be performed. Should be either "Body site" (default) or "Condition".
term

character. A valid term of ontology. Subsetting by this term then involves subsetting column to this term and all descendants of that term in the the chosen ontology and that are present in the chosen column of df.
ontology

an object of class ontology_index as defined in the ontologyIndex package. Typically obtained via getOntology.

Value

a data.frame with the chosen column restricted to descendants of the chosen term in the chosen ontology.

References

EFO: https://www.ebi.ac.uk/ols/ontologies/efo

UBERON: https://www.ebi.ac.uk/ols/ontologies/uberon

See Also

importBugSigDB, getOntology

Examples

# (1) Obtain BugSigDB data
 df <- importBugSigDB()

 # (2) Obtain ontology of interest as an R object
 uberon <- getOntology("uberon")

 # (3) High-level query on body site
 sdf <- subsetByOntology(df, 
                         column = "Body site",
                         term = "digestive system element",
                         ontology = uberon)
 table(sdf[,"Body site"])

Write microbe signatures to file in GMT format

Description

Functionality for writing microbe signatures to file in GMT format.

Usage

writeGMT(sigs, gmt.file, ...)

Arguments

sigs

A list of microbe signatures (character vectors of taxonomic IDs).
gmt.file

character. Path to output file in GMT format.
...

Arguments passed on to cat()

Value

none, writes to file.

References

GMT file format: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

Examples

bsdb <- importBugSigDB()
sigs <- getSignatures(bsdb)
writeGMT(sigs, gmt.file = "signatures.gmt")
file.remove("signatures.gmt")