searchAnalysis: Look up analysis accession IDs for one or more study or...

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

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

Description

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

Usage

searchAnalysis(x, ...)

## S4 method for signature '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.

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.

Value

Vector of analysis accession IDs.

Examples

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

# Retrieve analysis ids from study MGYS00005058
result <- searchAnalysis(mg, "studies", c("MGYS00005058"))

## Not run: 
# Retrieve all analysis ids from samples
result <- searchAnalysis(
    mg, "samples", c("SRS4392730", "SRS4392743"))

## End(Not run)

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