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# Package: Bios2cor
# This file is part of Bios2cor R package.
# Bios2cor is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# See the GNU General Public License at:
# http://www.gnu.org/licenses/
#
omes <- function(align, gap_ratio = 0.2) {
if ((gap_ratio < 0) | (gap_ratio > 1)) {
stop("gap_ratio must be in the [0,1] range.")
}
diag <- 0
msa<-align
MSA <- matrix(as.vector(unlist(msa)), ncol= length(msa[[1]]), byrow= TRUE)
nb_pos <- length(MSA[1,]) #number of positions in the alignment
nb_seq <- length(MSA[,1]) #number of sequences in the alignment
colnames(MSA)<-c(1:nb_pos)
pos_names <- colnames(MSA)
gap <- 1-gap_ratio #gap value indicates the minimal ratio of aa to nb_seq in the MSA
if (gap < 1/nb_seq) {
gap <- 1/nb_seq # positions must have at leat ONE aa to be taken into account (removes gap column)
}
names<-c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","-")
# Binary matrix indicating which amino acid is present or not at position i in the sequence j
AA<-lapply(1:nb_pos, function(i){
t(table(c(MSA[,i],names),row.names=c(1:(nb_seq+21))))[1:nb_seq, -1]
})
names<-c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
nb_aa <- length(names)
COV2<-matrix(0, ncol= nb_pos, nrow= nb_pos)
# Setting columns and rows names before matrix reduction
rownames(COV2)<-pos_names
colnames(COV2)<-pos_names
# Determining valid positions with correct gap ratio (equal to 1 - gap argument)
Valid_pos <- c()
for(i in 1:nb_pos){
mat_i <- AA[[i]] #matrix nb_seq*nb_aa
S_i <- colSums(AA[[i]])
Tot_i <- sum(S_i)
if (Tot_i/nb_seq >= gap) {
Valid_pos <- c(Valid_pos, i)
}
}
nb_Valid_pos <- length(Valid_pos)
# Calculating score for each valid position
for(i in 1:nb_Valid_pos){
pos_i <- Valid_pos[i] #current valid position
mat_i <- AA[[pos_i]] #matrix nb_seq*nb_aa
cat(paste("pos_i : ", pos_i, "\n"))
for(j in i:nb_Valid_pos){
pos_j <- Valid_pos[j]
mat_j <- AA[[pos_j]] #matrix nb_seq*nb_aa
#sequences in the alignment without gapped residues at positions i and k (no "-" in the positions i and k)
Valid<-which(AA[[pos_i]]%*%matrix(1, nrow= nb_aa)*AA[[pos_j]]%*%matrix(1, nrow= nb_aa)!=0)
#the number of sequences in the alignment without gapped residues at positions i and j (no "-" in the positions i and j)
n<-length(Valid)
Ex<-matrix(as.vector(t(AA[[pos_i]])%*%matrix(1,nrow= nb_seq)), ncol= nb_aa, nrow= nb_aa)*t(matrix(as.vector(t(AA[[pos_j]])%*%matrix(1,nrow= nb_seq)), ncol= nb_aa, nrow= nb_aa))/n
Obs<-t(AA[[pos_i]])%*%AA[[pos_j]]
COV2[pos_i, pos_j]<-sum((Obs-Ex)*(Obs-Ex)/n)
}
}
#Complete the second triangular part of the matrix
COV2<-COV2+t(COV2)
diag(COV2) <- diag
#Reducting the final correlation matrix to the valid positions
COV2 <- COV2[Valid_pos,]
COV2 <- COV2[,Valid_pos]
#Removing "Inf" values
COV2[is.infinite(COV2)] <- 0
COV2[is.na(COV2)] <- 0
res <- list()
# save matrix of score
res$score <- COV2
# compute and save matrix of Z_scores
# mean and stdev must be calculated on off diagonal elements
mean_up <- mean(COV2[upper.tri(COV2)])
stdev <- sd(COV2[upper.tri(COV2)])
COV2 <- (COV2-mean_up)/stdev
diag(COV2) <- diag
res$Zscore <- COV2
return(res)
}
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