rfamFamilySummary: Get a summary describing an Rfam family

Description Usage Arguments Value References Examples

View source: R/rfaRm_queryFunctions.R

Description

Gets a summary describing an Rfam family. The summary includes information regarding the number of sequences and species contained in the family, a brief description about the function of the family and the corresponding type of RNA.

Usage

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rfamFamilySummary(rfamFamily)

Arguments

rfamFamily

string with an Rfam family accession or ID for which a descriptive summary should be retrieved.

Value

A list containing the following elements that describe the Rfam family:

rfamReleaseNumber

Version of Rfam used in the query

numberSequencesSeedAlignment

Number of sequences used in the seed alignment of the Rfam family

sourceSeedAlignment

Published reference with the seed alignment of the Rfam family

numberSpecies

Number of species containing in their genomes sequences that belong to the Rfam family

RNAType

Keywords describing the type of RNA corresponding to the Rfam family

numberSequencesAll

Total number of sequences included in the Rfam family

structureSource

Description of the source for the secondary structure of the family (published, predicted) and PMID of the corresponding publication or prediction method if applicable

description

Descriptive name of the RNA included in the Rfam family

rfamAccession

Accession of the Rfam family

rfamID

ID of the Rfam family

comment

Short paragraph describing the characteristics and biological role of the Rfam family

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

https://docs.rfam.org/en/latest/api.html

Examples

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# Get a summary for the Rfam family with ID "FMN""

rfamFamilySummary("FMN")

# Get a summary for the Rfam family with accession "RF00174""

rfamFamilySummary("RF00174")

# Get a brief paragraph describing the Rfam family with accession "RF00174""

rfamFamilySummary("RF00174")$comment

LaraSellesVidal/rfaRm documentation built on Aug. 8, 2021, 7:25 p.m.