Description Usage Arguments Details Value Examples
View source: R/CMA.exported_functions.R
CMA_codon
Calculates the Direct Coupling, OMES and MI measurments of all pairwise positions of
a protein sequence based on an input MSA file of codon level sequences in fasta or sth format
1 2 3 4 5 | CMA_aa(
aa_alignment_file = system.file("extdata", "PF00014_full.fasta.test", package = "CMA"),
aa_alignment_file_type = "fasta",
seqnameorindex = "Q7K3Y9_DROME/661-715"
)
|
aa_alignment_file |
Input amino acid sequence alignment file name in a fasta or sth format |
aa_alignment_file_type |
Amino acid alignment file format (fasta or sth) |
seqnameorindex |
Id or index of the sequence as given in the amino acid sequence alignment file to evalute the correlated mutations for |
MI - **M**utual **I**nforamtion: 1. Convert table MI data to a matrix. 2. Execute the algorithm of MIp (below) 3. Returns the same table with i & j and but the column, MIp
Algorithm (based on http://bioinformatics.oxfordjournals.org/content/24/3/333.full): MI(a, mean(x)) = 1/m(Sum(MI(a, x))) where n is the number of columns in the alignment, m = n-1 for convenience, and the summation is over x=1 to n, x != a.
mean(MI) denotes the overall mean mutual information: mean(MI) = 2/(m*n)(Sum(MI(x, y))), where the indices run x=1 to m, y = x+1 to n.
The average product correction: APC(a, b) = (MI(a, mean(x))*MI(b, mean(x)))/mean(MI) Is an approximation to the background MI shared by positions a and b. MIp denotes the difference between total observed MI and the APC: MIp(a, b) = MI(a, b) - APC(a, b). In order to avoid negative values, values are shifted by adding the minimum
returns a data.frame of the measurements MI, OMES and DI at amino acid sequence level. See below for a description of the measurements.
1 2 3 4 5 6 | #Performing correlated mutatios annalysis at the
#amino acid level for Q7K3Y9_DROME/661-715 given PF00014 full alignment:
res.aa <- CMA_aa(aa_alignment_file = system.file("extdata",
"PF00014_full.fasta.test", package ="CMA"),
aa_alignment_file_type = "fasta",
seqnameorindex = "Q7K3Y9_DROME/661-715")
|
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