Calculate_Row_Weights: Calculate the sequence weights for all the rows in my...

In bgafun: BGAfun A method to identify specifity determining residues in protein families

Description

This will calculate the sequence weights for each group using the Heinkoff and Heinkoff method. Each residue in the sequence is assigned a weight depending on how unique it is in the column. The sequence weight is then the sum of these weights, and the total weight is the number of groups

Usage

 Calculate_Row_Weights(my_amino,label)

Arguments

my_amino	Matrix representation of alignment generated by convert\_aln\_amino
label	Vector or factor that shows the group representation for each sequence in the alignment

References

Henikoff, S. and J. G. Henikoff (1994). "Position-based sequence weights." J Mol Biol 243(4): 574-8.

Examples

library("bgafun")
data(LDH.amino.gapless)
data(LDH.groups)
LDH.weights=Calculate_Row_Weights(LDH.amino.gapless,LDH.groups)
sum(LDH.weights)

bgafun documentation built on April 28, 2020, 7:56 p.m.