Versatile function to retrieve raw results
Usage
getData(x, ...)
# S4 method for class '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
, ormydata
.- accession.type
A single character value specifying type of accession IDs (
accession
). Must be specified whenaccession
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.
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")