ptm (version 0.2.2)

site.type: Compute Shannon Entropy and Sort out the Sites

Description

Computes Shannon's entropies and performs a partition of the sites set.

Usage

site.type(target, species, th = 0.25)

Arguments

target

the KEGG identifier of the protein of interest.

species

a character vector containing the KEGG code for the species of interest.

th

value between 0 and 1 indicating the percentile driving the site partition.

Value

Returns a dataframe including the category of each site according to its variability.

Details

Each site can be classified according to their entropies into the following categories: invariant, pseudo-invariant, constrained, conservative, unconstrained, drastic.

See Also

msa(), custom.aln(), parse.hssp(), get.hssp(), shannon()

Examples

# NOT RUN {
site.type('hsa:4069', 'vertebrates')
# }