lmAlignment

object


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


The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.

Stefano de Pretis

LowMACA

LowMACA - Low frequency Mutation Analysis via Consensus Alignment

lmAlignment function

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

Show Alignment Results from a LowMACA object

a list of two objects
    <ul><li>DIST_MAT</li></ul>{ a matrix of the pairwise similarities between sequences 
                      as resulted after the multiple alignment (from 0% to 100%)}
      <item>SUMMARY_SCORE</item>{ a data.frame containing summary descriptives of the distance matrix}
      <item>CLUSTAL</item>{ an object of class "AAMultipleAlignment" as provided by Biostrings R package}
      <item>df</item>{ a dataframe containing the predicted consesus sequence and the trident conservation score at every position}

lmAlignment: Show Alignment Results from a LowMACA object

Description

Usage

Arguments

Value

See Also

Examples