GetInfProfile: Information content profile of an alignment

Description Usage Arguments Value Author(s) References Examples

View source: R/GetInfProfile.R

Description

GetInfProfile computes the information content at each position of an alignment.

Usage

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Arguments

seqs

DNAStringSet or AAStringSet with the haplotype alignment.

nr

An optional numeric vector with the haplotype counts to take into account the information content of each position in the alignment.

Value

Returns a numeric vector whose length is equal to the length of the alignment. Each value corresponds to the information content of each position in the alignment.

Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

References

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

Examples

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# Load the alignment.
filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")

# Compute the alignment's IC profile.
GetInfProfile(lst$hseqs)
# Also taking into account haplotype frequencies.
GetInfProfile(lst$hseqs,lst$nr)

VHIRHepatiques/QSutils documentation built on Oct. 24, 2018, 12:06 p.m.