lmAlignment: Show Alignment Results from a LowMACA object

In ste-depo/LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Show Alignment Results from a LowMACA object

Description

Method for objects of class LowMACA. It can show the results of the alignment procedure that has been performed on the LowMACA object

Usage

lmAlignment(object)

Arguments

object

object of class LowMaca

Value

A list containing the following elements:

• ALIGNMENT an object of class data.frame containing the mapping of the position of the original amino acids to the consensus sequence

• SCORE a list of two objects

  • DIST_MAT a matrix of the pairwise similarities between sequences as resulted after the multiple alignment (from 0% to 100%)

  • SUMMARY_SCORE a data.frame containing summary descriptives of the distance matrix

  • CLUSTAL an object of class "AAMultipleAlignment" as provided by Biostrings R package

  • df a dataframe containing the predicted consesus sequence and the trident conservation score at every position

Author(s)

Stefano de Pretis, Giorgio Melloni

See Also

alignSequences

Examples

data('lmObj')
str(lmAlignment(lmObj))

ste-depo/LowMACA documentation built on Oct. 15, 2022, 11:53 p.m.