Package 'HoloFoodR'

Title: R interface to EBI HoloFood resource
Description: Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.
Authors: Tuomas Borman [aut, cre] , Leo Lahti [aut]
Maintainer: Tuomas Borman <[email protected]>
License: Artistic-2.0 | file LICENSE
Version: 0.99.8
Built: 2024-07-28 03:50:29 UTC
Source: https://github.com/bioc/HoloFoodR

Help Index

Search HoloFood database for animals, genome catalogues, samples, or viral catalogues

Description

Search HoloFood database for animals, genome catalogues, samples, or viral catalogues

Usage

doQuery(type, flatten = TRUE, ...)

Arguments

type

Character scalar specifying the type of data to query. Must be one of the following options: "animals", "genome-catalogues", "samples" or "viral-catalogues".
flatten

Logical scalar specifying whether to flatten the resulting data.frame. This means that columns with multiple values are separated to multiple columns. (Default: TRUE)
...

optional arguments:

  • max.hits NULL or integer scalar specifying the maximum number of results to fetch. When NULL, all results are fetched. (Default: NULL)

  • spread.sample.types Logical scalar specifying whether to create spread sample types column of animals data. In animals data, sample types column might have multiple values that might be hard to explore. This argument specifies whether to create presence/absence table from sample types. (Default: TRUE)

  • use.cache Logical scalar specifying whether to use cache. (Default: FALSE)

  • cache.dir Character scalar specifying cache directory. (Default: tempdir())

  • clear.cache Logical scalar specifying whether to remove and clear cache (Default: FALSE)

Details

doQuery is a flexible query function which can be utilized to search available animals, genome catalogues, samples, or viral catalogues. Search results can be filtered; for example, animals can be filtered based on available samples. See [Api browser](https://www.holofooddata.org/api/docs) for information on filters. You can find help on customizing queries from [here](https://emg-docs.readthedocs.io/en/latest/api.html#customising-queries).

Value

data.frame

Examples

# Find animals results. The maximum amount of results is 100. Use filter
# so that only chicken is searched.
res <- doQuery("animals", max.hits = 100, system = "chicken")
head(res)

Get data from HoloFood database

Description

Get data from HoloFood database

Usage

getData(
  type = NULL,
  accession.type = NULL,
  accession = NULL,
  flatten = FALSE,
  ...
)

Arguments

type

NULL or character scalar specifying the type of data to query. Must be one of the following options: "analysis-summaries", "animals", "genome-catalogues", "samples", "sample_metadata_markers" or "viral-catalogues". When genome or viral catalogues is fetched by their accession ID, the type can also be "genomes" or "fragments". (Default: NULL)
accession.type

NULL or character scalar specifying the type of accession IDs. Must be one of the following options: "animals", "genome-catalogues", "samples" or "viral-catalogues". (Default: NULL)
accession

NULL or character vector specifying the accession IDs of type accession.type. (Default: NULL)
flatten

Logical scalar specifying whether to flatten the resulting data.frame. This means that columns with multiple values are separated to multiple columns. (Default: FALSE)
...

optional arguments:

  • max.hits NULL or integer scalar specifying the maximum number of results to fetch. When NULL, all results are fetched. (Default: NULL)

  • use.cache Logical scalar specifying whether to use cache (Default: FALSE)

  • cache.dir Character scalar specifying cache directory. (Default: tempdir())

  • clear.cache Logical scalar specifying whether to remove and clear cache (Default: FALSE)

Details

With getData, you can fetch data from the database. Compared to getResult, this function is more flexible since it can fetch any kind of data from the database. However, this function returns the data without further wrangling as list or data.frame which are not optimized format for fetching data on samples.

Search results can be filtered; for example, animals can be filtered based on available samples. See [Api browser](https://www.holofooddata.org/api/docs) for information on filters. You can find help on customizing queries from [here](https://emg-docs.readthedocs.io/en/latest/api.html#customising-queries).

Value

list or data.frame

See Also

getResult

Examples

# Find genome catalogues
catalogues <- getData(type = "genome-catalogues")
head(catalogues)

# Find genomes based on certain genome catalogue iD
res <- getData(
    type = "genomes", accession.type = "genome-catalogues",
    accession = catalogues[1, "id"], max.hits = 100)
head(res)

Get metabolomic data from MetaboLights database

Description

Get metabolomic data from MetaboLights database

Usage

getMetaboLights(url, ...)

Arguments

url

character vector specifying the URL address of study in MetaboLights database.
...

optional arguments:

  • cache.dir Character scalar specifying directory where downloaded file is stored. (Default: tempdir())

Details

The HoloFood database primarily comprises targeted metabolomic data, omitting non-targeted metabolomic information. Nonetheless, it features URLs linking to studies within the MetaboLights database. This functionality enables users to access non-targeted metabolomic data. The function returns a structured list encompassing data frames for study metadata, assay metadata, and assay.

Value

list

See Also

getResult getData

Examples

# This example is not run, because the server fails to respond sometimes.

url <- "https://www.ebi.ac.uk/metabolights/ws/studies/MTBLS4381"

if( FALSE ){
    res <- getMetaboLights(url)
    names(res)
    head(res[["feat_meta"]])
}

Get data on samples from HoloFood database

Description

Get data on samples from HoloFood database

Usage

getResult(accession, get.metabolomic = FALSE, ...)

Arguments

accession

Character vector specifying the accession IDs of type samples.
get.metabolomic

Logical scalar specifying whether to retrieve metabolomic data from MetaboLights database. (Default: FALSE)
...

optional arguments:

  • use.cache Logical scalar specifying whether to use cache. Note that when get.metabolomic = TRUE is specified, the file from the MetaboLights is stored in the local system to the location specified by cache.dir despite of the value of use.cache. (Default: FALSE)

  • cache.dir Character scalar specifying cache directory. (Default: tempdir())

  • clear.cache Logical scalar specifying whether to use.cache (Default: FALSE)

  • assay.type Character scalar specifying the name of assay in resulting TreeSummarizedExperiment object. (Default: "counts")

Details

With getResult, you can fetch data on samples from the HoloFood database. Compared to getData, this function is more convenient for fetching the samples data because it converts the data to MultiAssayExperiment where different omics are stored as TreeSummarizedExperiment objects which are optimized for downstream analytics. Columns of returned MultiAssayExperiment are individual animals. These columns are linked with individual samples that are stored in TreeSummarizedExperiment objects.

The HoloFood database lacks non-targeted metabolomic data but fetched from MetaboLights resource. The function getResult facilitates the automatic retrieval of metabolomic data and its integration with other datasets from HoloFood.

Furthermore, while the HoloFoodR database does not include metagenomic assembly data, users can access such data from the MGnify database. The MGnifyR package provides a convenient interface for accessing this database. By employing MGnifyR::getResult(), users can obtain data formatted as a MultiAssayExperiment object, containing multiple TreeSummarizedExperiment objects. Consequently, data from both HoloFood and MGnify databases are inherently compatible for subsequent downstream analysis.

Value

MultiAssayExperiment

See Also

getData TreeSummarizedExperiment MultiAssayExperiment MGnifyR:getResult

Examples

# Find samples on certain animal
samples <- doQuery("samples", animal_accession = "SAMEA112904746")

# Get the data
mae <- getResult(samples[["accession"]])
mae

HoloFoodR package

Description

HoloFoodR implements an interface to the EBI HoloFood database. See the vignette for a general introduction to this package, [about HoloFood](https://www.holofood.eu/) for general HoloFood information, and [API documentation](https://docs.holofooddata.org/api.html) for details on the JSONAPI implementation.

Author(s)

Maintainer: Tuomas Borman [email protected] (ORCID)

Authors:

See Also

TreeSummarizedExperiment MultiAssayExperiment