Look up analysis accession IDs for one or more study or sample accessions

Usage

searchAnalysis(x, ...)

# S4 method for class 'MgnifyClient'
searchAnalysis(x, type, accession, ...)

Arguments

x: A MgnifyClient object.
...: Optional arguments; not currently used.
type: A single character value specifying a type of accession IDs specified by accession. Must be "studies" or "samples".
accession: A single character value or a vector of character values specifying study or sample accession IDs that are used to retrieve analyses IDs.

Value

Vector of analysis accession IDs.

Details

Retrieve analysis accession IDs associated with the supplied study or sample accession. In MGnify, an analysis accession refers to a certain pipeline analysis, such as specific 16S rRNA or shotgun metagenomic mapping. Studies can include multiple samples, and each sample can undergo multiple analyses using these pipelines. Each analysis is identified by a unique accession ID, allowing precise tracking and retrieval of analysis results within the MGnify database.

Examples

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

# Retrieve analysis ids from study MGYS00005058
result <- searchAnalysis(mg, "studies", c("MGYS00005058"))
#> Fetching analyses...
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%

if (FALSE) { # \dontrun{
# Retrieve all analysis ids from samples
result <- searchAnalysis(
    mg, "samples", c("SRS4392730", "SRS4392743"))
} # }