Description Usage Arguments Details Value Author(s) References See Also Examples
The function returns the entropy value for a nucleotide sequence provided as a vector of bases.
1 | CalcEntropy.seq(Seq)
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Seq |
a vector of nucleotide bases (See examples). |
In case some bases are unknown ".", the entropy is calculated with the other bases (including gaps "-") but over the total sequence length.
This function returns a numeric value for the calculated entropy.
Alban Ramette
The entropy function is defined in: Eren et al. 2013 Methods in Ecology and Evolution. 4,1111-??1119. doi: 10.1111/2041-210X.12114. http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12114/pdf
CalcEntropy.word
1 2 3 4 5 6 7 8 9 | Seq1="AAAAAAAA" # this is not the correct input
Seq2="AACCTTGG" # this is not the correct input
Seq3=c(rep("A",8)) # this is the correct type of input
Seq4=c(rep("A",2),rep("C",2),rep("T",2),rep("G",2)) # this is the correct type of input
CalcEntropy.seq(Seq1) # 0
CalcEntropy.seq(Seq2) # 0
CalcEntropy.seq(Seq3) # 0
CalcEntropy.seq(Seq4) # 2
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