Escore_conservativity {BALCONY} | R Documentation |
This function facilitates the calculation of Escore conservation metric (in amino acid or group mode)
Escore_conservativity(alignment, grouping_method = NULL, weights = NULL,pseudo_counts=F)
alignment |
Alignment data read with |
grouping_method |
(optional) A string which specifies the grouping method to be used. One of following: 'substitution_matrix', 'polarity', 'size', 'aromaticity', default: NULL |
weights |
(optional) A vector of length equal number of sequences in the alignment object with weights to overcome the taxonomic bias in the conservation analysis. |
pseudo_counts |
(optional) A logical indicating if pseudo-counts should be added to the MSA. Pseudo-counts can be used only in non-group mode and without weights. Using these options with pseudo-counts will be suppressed. Default: FALSE |
The conservativity score is calculated according to the following formula:
P(i) = max(p(i))/n(i)
Pnorm(i) = P(i)/max(P)
score = -ln(P_norm(i))/max(-ln(P_norm))
where:
p(i) - amino acids frequency on i-th position where gaps are included
n(i) - amino acids count on i-th position where gaps are excluded
conservation_score |
A vector of length equal to the length of aligned sequences |
Also, this function originally calculates the entropy values which can be used to estimate the conservativity score according to the following formula:
conservation = 1 - entropy
Alicja Pluciennik & Michal Stolarczyk
data("small_alignment") conservation_score = Escore_conservativity(alignment)