CMA_codon: Correlated mutation analysis at the codon sequence level by...

In etaijacob/CMA: An R package for correlated mutation analysis using both codon and amino acid levels

Description

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

Usage

CMA_codon(
  aa_alignment_file = system.file("extdata", "PF00014_full.fasta.test", package = "CMA"),
  aa_alignment_file_type = "fasta",
  codon_alignment_file = system.file("extdata", "PF00014_full.fasta.test.tranalignout",
    package = "CMA"),
  codon_alignment_file_type = "fasta",
  seqnameorindex = "Q7K3Y9_DROME/661-715"
)

Arguments

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)
codon_alignment_file	Input codon sequence alignment file name in a fasta or sth format
codon_alignment_file_type	Codon 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

Details

MI - **M**utual **I**nforamtion calc MIp by: 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

Value

returns a data.frame of the measurements MI, OMES and DI at codon sequence level. See below for a description of the measurements.

Examples

#Performing correlated mutatios annalysis at the codon level for Q7K3Y9_DROME/661-715 given
#PF00014 full alignment:
res.codon <- CMA_codon(aa_alignment_file = system.file("extdata",
                                                       "PF00014_full.fasta.test",
                                                       package ="CMA"),
                       aa_alignment_file_type = "fasta",
                       codon_alignment_file = system.file("extdata",
                                                          "PF00014_full.fasta.test.tranalignout",
                                                          package ="CMA"),
                       codon_alignment_file_type = "fasta",
                       seqnameorindex = "Q7K3Y9_DROME/661-715")

etaijacob/CMA documentation built on Dec. 27, 2019, 4:17 p.m.