getData: Versatile function to retrieve raw results

In beadyallen/MGnifyR: R interface to EBI MGnify metagenomics resource

Versatile function to retrieve raw results

Description

Versatile function to retrieve raw results

Usage

getData(x, ...)

## S4 method for signature 'MgnifyClient'
getData(x, type, accession.type = NULL, accession = NULL, as.df = TRUE, ...)

Arguments

x	A MgnifyClient object.
...	optional arguments fed to internal functions.
type	A single character value specifying the type of data retrieve. Must be one of the following options: studies, samples, runs, analyses, biomes, assemblies, super-studies, experiment-types, pipelines, pipeline-tools, publications, genomes, genome-search, genome-search/gather, genome-catalogues, genomeset, cogs, kegg-modules, kegg-classes, antismash-geneclusters, annotations/go-terms, annotations/interpro-identifiers, annotations/kegg-modules, annotations/pfam-entries, annotations/kegg-orthologs, annotations/genome-properties, annotations/antismash-gene-clusters, annotations/organisms, or mydata.
accession.type	A single character value specifying type of accession IDs (accession). Must be specified when accession is specified. (By default: accession.type = NULL)
accession	A single character value or a vector of character values specifying accession IDs to return results for. (By default: accession = NULL)
as.df	A single boolean value specifying whether to return the results as a data.frame or leave as a nested list. (By default: as.df = TRUE)

Details

This function returns data from MGnify database. Compared to getResult, this function allows more flexible framework for fetching the data. However, there are drawbacks: for counts data, getResult returns optimally structured data container which is easier for downstream analysis. getData returns raw data from the database. However, if you want to retrieve data on pipelines or publications, for instance, getResult is not suitable for it, and getData can be utilized instead.

Value

data.frame or list

See Also

getResult

Examples

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

# Find kegg modules for certain analysis
df <- getData(
    mg, type = "kegg-modules",
    accession = "MGYA00642773", accession.type = "analyses")

beadyallen/MGnifyR documentation built on Dec. 3, 2024, 8:21 a.m.