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

Source: R/doQuery.R
doQuery.Rd

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)

Value

data.frame

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).

Examples


# Find animals results. The maximum amount of results is 100. Use filter
# so that only chicken is searched. (See details on customizing queries)
res <- doQuery("animals", max.hits = 100, system = "chicken")
head(res)
#>        accession  system                                   canonical_url
#> 1 SAMEA112904733 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904733
#> 2 SAMEA112904734 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904734
#> 3 SAMEA112904735 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904735
#> 4 SAMEA112904736 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904736
#> 5 SAMEA112904737 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904737
#> 6 SAMEA112904738 chicken https://www.ebi.ac.uk/biosamples/SAMEA112904738
#>   histological host_genomic inflammatory_markers metabolomic
#> 1        FALSE         TRUE                FALSE       FALSE
#> 2         TRUE         TRUE                 TRUE       FALSE
#> 3         TRUE         TRUE                 TRUE       FALSE
#> 4        FALSE         TRUE                FALSE       FALSE
#> 5         TRUE         TRUE                 TRUE       FALSE
#> 6        FALSE         TRUE                FALSE       FALSE
#>   metabolomic_targeted metagenomic_assembly metatranscriptomic transcriptomic
#> 1                FALSE                 TRUE              FALSE          FALSE
#> 2                 TRUE                 TRUE               TRUE           TRUE
#> 3                 TRUE                 TRUE              FALSE           TRUE
#> 4                FALSE                 TRUE              FALSE          FALSE
#> 5                 TRUE                 TRUE               TRUE           TRUE
#> 6                 TRUE                 TRUE              FALSE          FALSE