add_pseudo_counts: Add pseudo counts to amino acid matrix based on defined...

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

Description

This function will add pseudo counts to binary amino acid matrix based on the defined groups. It is used to minimise the effect of small sample size. The method of Henikoff and Henikoff is used to calculate the pseudocounts An alternative method is to simply add 1 to the binary matrix

Usage

 add_pseudo_counts(amino,groups)

Arguments

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

Examples

library(bgafun)
data(LDH.amino.gapless)
data(LDH.groups)
LDH.pseudo=LDH.amino.gapless+1
#or use the function 
LDH.pseudo=add_pseudo_counts(LDH.amino.gapless,LDH.groups)

Example output

Loading required package: made4
Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
Loading required package: seqinr

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