getPropCorr: Get amino acid property wise correlations of co-evolving...

In aaSEA: Amino Acid Substitution Effect Analyser

Description

Get amino acid property wise correlations of co-evolving columns of a multiple sequence alignment

Usage

getPropCorr(selMat, propertyDF = "Cruciani", propertyIndex = 1)

Arguments

selMat	A subset matrix of original multiple sequence alignment with significant correlations identified with 'getCorSites' function
propertyDF	One of the amino acid property data frames. viz. Cruciani, Fasgai, Kidera, AAindex. Default is Cruciani properties
propertyIndex	Specific property row number from the data frame of propertyDF

Value

A data frame of four columns viz. Pos1, Pos2, Cor and p Value. Results are filtered to find position pairs with correlations above 0.8 and below -0.8

Examples

selMatLoc <- system.file("extdata", "selMat.rda", package = "aaSEA")
selMat <- readRDS(selMatLoc)
getPropCorr(selMat = selMat, propertyDF = "Cruciani", propertyIndex = 1) 

aaSEA documentation built on Nov. 9, 2019, 5:07 p.m.