Get pre-configured tables from OrthoMCL-DB — getPreconfiguredTableOrthomcl • plasmoRUtils

A convenience function to quickly fetch preconfigured tables from OrthoMCL-DB. This function can be used to map old OG IDs to new and vice-versa given a vector of OG IDs. If no IDs are provided, the entire data table fetched from the database is returned and a copy of it is cached to reduce the next query time.

Usage

getPreconfiguredTableOrthomcl(
  og_ids = NULL,
  customField = "previousGroups",
  api_key = Sys.getenv("VEUPATHDB_API_KEY"),
  timeout = 60,
  max_tries = 3,
  refresh = FALSE
)

Arguments

og_ids

Orthogroup IDs.

customField

Preconfigured table to be downloaded from OrthoMCL.

api_key

Character. VEuPathDB API key used for authentication. By default, the value is obtained from the VEUPATHDB_API_KEY environment variable.

timeout

Timeout time in seconds.

max_tries

Maximum retries allowed.

refresh

Logical. If TRUE, ignores any locally cached copy and downloads the requested table again from OrthoMCL. Defaults to FALSE.

"TaxonCounts": Phyletic Distribution of Proteins
"PhyleticDistributionCounts": Phyletic Distribution clade abundance
"previousGroups": All previous groups. "Default"
"GroupStat": Group Statistics
"SimilarGroup": Similar Groups
"EcNumber": Summary of EC Numbers
"PFams": Summary of Pfam domains
"ProteinPFams": PFam Architecture of Each Protein
"KeywordFrequency": Keyword Frequency

Value

A data frame.

Examples

if (FALSE) { # \dontrun{
df <- getPreconfiguredTableOrthomcl("OG3_10277")
df <- getPreconfiguredTableOrthomcl(customField = "SimilarGroup")
} # }