Show Alignment Results from a LowMACA object

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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

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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

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