rfamCovarianceModel: Get the covariance model associated to an Rfam family
In LaraSellesVidal/rfaRm: An R interface to the Rfam database

Description Usage Arguments Value References Examples

Gets the covariance model generated with the Infernal software of the Rfam family. Covariance models can be used in Infernal to search through a list of sequences for high-scoring hits to the models. If a filename is provided, the covariance model will be saved to the specified path.

1	rfamCovarianceModel(rfamFamily, filename=NULL)

`rfamFamily`	string with an Rfam family accession or ID for which the covariance model should be retrieved.
`filename`	string indicating a path to which the covariance model should be written. In the default behaviour, filename=NULL, the covariance model will not be saved into any file, and instead will only be returned as a string.

A string with the covariance model of the Rfam family in the Infernal format. If a filename is provided, the covariance model file will also be written to the specified path.

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

Eric P Nawrocki, Sean R Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, Volume 29, Issue 22, 15 November 2013, Pages 2933–2935, https://doi.org/10.1093/bioinformatics/btt509

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

http://eddylab.org/infernal/Userguide.pdf

# Retrieve the covariance model for the Rfam family with ID "FMN" and save it
# to a file

rfamCovarianceModel("FMN", filename="FMNcovarianceModel.cm")

# Retrieve the covariance model for the Rfam family with accession "RF00174" and
# save it to a file

rfamCovarianceModel("RF00174", filename="RF00174covarianceModel.cm")