structureMismatchScore: Scores how a basepair structure fits a sequence

In R4RNA: An R package for RNA visualization and analysis

Description

Calculates a score that indicates how badly a set of basepairs (i.e. a secondary structure) fits with a sequence. A perfect fit is a structure where all basepairs form valid basepairs (A:U, G:C, G:U, and equivalents) and has a score of 0. Each basepair that forms a non-canonical pairing or pairs to gaps increases the score by 1, and each base-pair with a single-sided gap increases the score by 2.

Usage

    structureMismatchScore(msa, helix, one.gap.penalty = 2, two.gap.penalty = 2,
                 invalid.penalty = 1)

Arguments

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.
helix	A helix data.frame
one.gap.penalty	Penalty score for basepairs with one of the bases being a gap
two.gap.penalty	Penalty score for basepairs with both bases being a gaps
invalid.penalty	Penalty score for non-canonical basepairs

Value

Returns an array of mismatch scores.

Author(s)

Jeff Proctor, Daniel Lai

Examples

    data(helix)
    mismatch <- structureMismatchScore(fasta, known)
    
    # Sort by increasing mismatch
    sorted_fasta <- fasta[order(mismatch)]

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

R4RNA documentation built on Nov. 8, 2020, 5:15 p.m.