add_pseudo_counts {bgafun} | R Documentation |
Add pseudo counts to amino acid matrix based on defined groups
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)
[Package
bgafun version 1.4.0
Index]