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Get microbial and/or functional profiling data for a list of accessions

Source: R/AllGenerics.R, R/getResult.R
getResult.Rd

Get microbial and/or functional profiling data for a list of accessions

Usage

getResult(x, ...)

# S4 method for class 'MgnifyClient'
getResult(
  x,
  accession,
  get.taxa = TRUE,
  get.func = TRUE,
  output = "TreeSE",
  ...
)

Arguments

x

A MgnifyClient object.

...

optional arguments:

  • taxa.su A single character value specifying which taxa subunit results should be selected. Currently, taxonomy assignments in the MGnify pipelines rely on rRNA matches to existing databases (GreenGenes and SILVA), with later pipelines checking both the SSU and LSU portions of the rRNA sequence. taxa.su allows then selection of either the Small subunit ("SSU") or Large subunit ("LSU") results in the final TreeSummarizedExperiment object. Older pipeline versions do not report results for both subunits, and thus for some accessions this value will have no effect.

  • get.tree A single boolean value specifying whether to include available phylogenetic trees in the TreeSummarizedExperiment object. Available when get.taxa = TRUE. (By default: get.tree = TRUE)

  • as.df A single boolean value enabled when output = "list". The argument specifies whether return functional data as a named list (one entry per element in the output list) of data.frames, with each data.frame containing results for all requested accessions. If FALSE, the function returns a list of lists, each element consisting of results for a single accession. (By default: as.df = TRUE)

  • bulk.dl A single boolean value specifying should MGnifyR attempt to speed things up by downloading relevant studies TSV results and only extracting the required columns, rather than using the JSONAPI interface. When getting results where multiple accessions share the same study, this option may result in significantly faster processing. However, there appear to be (quite a few) cases in the database where the TSV result columns do NOT match the expected accession names. This will hopefully be fixed in the future, but for now bulk.dl defaults to TRUE. When it does work, it can be orders of magnitude more efficient. (By default: buld_dl = TRUE)

accession

A single character value or a vector of character values specifying accession IDs to return results for.

get.taxa

A boolean value specifying whether to retrieve taxonomy data (OTU table). See taxa.su for specifying taxonomy type. The data is retrieved as BIOM files which are subsequently parsed. (By default: get.taxa = TRUE)

get.func

A boolean value or a single character value or a vector character values specifying functional analysis types to retrieve. If get.func = TRUE, all available functional datatypes are retrieved, and if FALSE, functional data is not retrieved. The current list of available types is "antismash-gene-clusters", "go-slim", "go-terms", "interpro-identifiers", "taxonomy", "taxonomy-itsonedb", "taxonomy-itsunite", "taxonomy-lsu", and "taxonomy-ssu". Note that depending on the particular analysis type, pipeline version etc., not all functional results will be available. Furthermore, taxonomy is also available via get.func, and loading the data might be considerable faster if bulk.dl = TRUE. However, phylogeny is available only via get.taxa. (By default: get.func = TRUE)

output

A single character value specifying the format of an output. Must be one of the following options: "TreeSE", "list", or "phyloseq". (By default: output = "TreeSE")

Value

If only taxonomy data is retrieved, the result is returned in TreeSummarizedExperiment object by default. The result can also be returned as a phyloseq object or as a list of data.frames. Note that phyloseq object can include only one phylogenetic tree meaning that some taxa might be lost when data is subsetted based on tree.

When functional data is retrieved in addition to taxonomy data, the result is returned as a MultiAssayExperiment object. Other options are a list containing phyloseq object and data.frames or just data.frames.

Functional data can be returned as a MultiAssayExperiment object or as a list of data.frames.

Details

Given a set of analysis accessions and collection of annotation types, the function queries the MGNify API and returns the results. This function is convenient for retrieving highly structured (analysis vs counts) data on certain instances. For example, BIOM files are downloaded automatically. If you want just to retrieve raw data from the database, see getData.

See also

getData

Examples

# Create a client object
mg <- MgnifyClient(useCache = FALSE)

# Get OTU tables as TreeSE
accession_list <- c("MGYA00377505")
tse <- getResult(mg, accession_list, get.func=FALSE, get.taxa=TRUE)
#> Fetching taxonomy data...
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
#> Merging with full join...
#> 1/1
#> 

if (FALSE) { # \dontrun{
# Get functional data along with OTU tables as MAE
mae <- getResult(mg, accession_list, get.func=TRUE, get.taxa=TRUE)

# Get same data as list
list <- getResult(
    mg, accession_list, get.func=TRUE, get.taxa=TRUE, output = "list",
    as.df = TRUE, use.cache = TRUE)
} # }