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Get pre-configured tables from OrthoMCL-DB

Source: R/getPreconfiguredTableOrthomcl.R
getPreconfiguredTableOrthomcl.Rd

A convenience function to quickly fetch preconfigured table of 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, entire data tables fetched from the database will be returned, which can be manipulated or processed further as per user need.

Usage

getPreconfiguredTableOrthomcl(
  og_ids = NULL,
  customField = "previousGroups",
  timeout = 60,
  max_tries = 3
)

Arguments

og_ids

Orthogroup IDs.

customField

Preconfigured tables to be downloaded from OrthoMCL.

timeout

Timeout time in seconds

max_tries

Maximum retries allowed.

  • "TaxonCounts": Phlyetic 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")
} # }