R4RNA (version 1.0.0)

Alignment Statistics: Compute statistics for a multiple sequence alignments

Description

Functions to compute covariation, percent identity conservation, and percent canonical basepairs given a multiple sequence alignment and optionally a secondary structure. Statistics can be computed for a single base, basepair, helix or entire alignment.

Usage

baseConservation(msa, pos)
    basepairConservation(msa, pos.5p, pos.3p) basepairCovariation(msa, pos.5p, pos.3p)  basepairCanonical(msa, pos.5p, pos.3p)
    helixConservation(helix, msa) helixCovariation(helix, msa) helixCanonical(helix, msa) 
    alignmentConservation(msa) alignmentCovariation(msa, helix) alignmentCanonical(msa, helix)  alignmentPercentGaps(msa)

Arguments

helix

A helix data.frame

msa

A multiple sequence alignment. Can be either a Biostrings XStringSet object or a named array of strings like ones obtained from converting XStringSet with as.character.

pos, pos.5p, pos.3p

Positions of bases or basepairs for which statistics shall be calculated for.

Value

baseConservation, basepairConservation, basepairCovariation, basepairCanonical, alignmentConservation, alignmentCovariation, and alignmentCanonical return a single decimal value.helixConservation, helixCovariation, helixCanonical return a list of values whose length equals the number of rows in helix.alignmentPercentGaps returns a list of values whose length equals the number of sequences in the multiple sequence alignment.

Details

Conservation values have a range of [0, 1], where 0 is the absence of primary sequence conservation (all bases different), and 1 is full primary sequence conservation (all bases identical). Canonical values have a range of [0, 1], where 0 is a complete lack of basepair potential, and 1 indicates that all basepairs are valid

Covariation values have a range of [-2, 2], where -2 is a complete lack of basepair potential and sequence conservation, 0 is complete sequence conservation regardless of basepairing potential, and 2 is a complete lack of sequence conservation but maintaining full basepair potential.

helix values are average of base/basepair values, and the alignment values are averages of helices or all columns depending on whether the helix argument is required.

alignmentPercentGaps simply returns the percentage of nucleotides that are gaps in a sequence for each sequence of the alignment.

Examples

    data(helix)
    
    baseConservation(fasta, 9)

    basepairConservation(fasta, 9, 18)
    basepairCovariation(fasta, 9, 18) 
    basepairCanonical(fasta, 9, 18)

    helixConservation(helix, fasta)
    helixCovariation(helix, fasta)
    helixCanonical(helix, fasta)

    alignmentConservation(fasta)
    alignmentCovariation(fasta, helix)
    alignmentCanonical(fasta, helix)

    alignmentPercentGaps(fasta)