BALCONY (version 0.2.10)

calculate_pseudo_counts: Calculate pseudo counts for alignment

Description

This function calculates pseudo-counts (as shown in Henikoff et al. (1996)) for an alignment with the use of substitution matrices. It is recommended to estimate amino acid frequencies for alignments with small number of sequences (in order to calculate reliable entropy scores)

Usage

calculate_pseudo_counts(alignment, substitution_mtx)

Arguments

alignment

alignment loaded with read.alignment

substitution_mtx

Matrix with amino acids substitution frequencies. Default: GONNET

Value

pseudoCounts

Matrix with pseudo counts of size 21x number of alignment columns

References

Henikoff et al.(1996) Using substitution probabilities to improve position-specific scoring matrices, Bioinformatics, 12, 135<U+2013>143 Claverie (1994) Some useful statistical properties of position-weight matrices. Comput. Chem., 18, 287-293

Examples

# NOT RUN {
data("alignment")
PC <- calculate_pseudo_counts(alignment)
# }