GetInfProfile: Information content profile of an alignment
In QSutils: Quasispecies Diversity

Description Usage Arguments Value Author(s) References Examples

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

1	GetInfProfile(seqs,nr=NULL)

`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.

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.

Mercedes Guerrero-Murillo and Josep Gregori

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.

# 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)