calculate_pseudo_counts: Calculate pseudo counts for alignment

In BALCONY: Better ALignment CONsensus analYsis

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

Note

Please note that when using other scoring matrix user needs to make sure that all alignment symbols are present there. Missing symbol will issue an error.

Author(s)

Alicja Płuciennik & Michał Stolarczyk

References

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

Examples

data("alignment")
PC <- calculate_pseudo_counts(alignment)

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 

BALCONY documentation built on May 1, 2019, 10:31 p.m.