Position Weight Matrix

Position Weight Matrix

Στην συνέχεια μετατρέπουμε τα strings σε vectors

## IT's a list!
unlist(a.tmp)

[1] "K" "A" "L" "I" "M" "E" "R" "A"

Που θα σωσουμε τα νέα vectors? Σε πίνακα…

m1 = matrix("", nrow=nrow(a), ncol=9)
m1

for(i in 1:nrow(a)){
  v = unlist(strsplit(a[i,], split=""))
  m1[i,] = v
}
m1

countmat = matrix(0, nrow=4, ncol=9)
rownames(countmat) = c("A", "C", "G", "T")
for(i in 1:nrow(m1)){
  for(j in 1:ncol(m1)){
    mychar = m1[i,j]
    ##print(mychar)
    countmat[mychar, j] = countmat[mychar, j] + 1
  }
}
countmat

Ας μετατρέψουμε τώρα τον countmat σε συχνότητες

freqmat

  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
A  0.3  0.6  0.1    0    0  0.6  0.7  0.2  0.1
C  0.2  0.2  0.1    0    0  0.2  0.1  0.1  0.2
G  0.1  0.1  0.7    1    0  0.1  0.1  0.5  0.1
T  0.4  0.1  0.1    0    1  0.1  0.1  0.2  0.6

Μετατροπή σε log2 προς expected values

pwm

        [,1]       [,2]      [,3]      [,4]      [,5]       [,6]      [,7]
A  0.2630356  1.2630350 -1.321924 -19.93157 -19.93157  1.2630350  1.485427
C -0.3219263 -0.3219263 -1.321924 -19.93157 -19.93157 -0.3219263 -1.321924
G -1.3219245 -1.3219245  1.485427   2.00000 -19.93157 -1.3219245 -1.321924
T  0.6780728 -1.3219245 -1.321924 -19.93157   2.00000 -1.3219245 -1.321924
        [,8]       [,9]
A -0.3219263 -1.3219245
C -1.3219245 -0.3219263
G  1.0000007 -1.3219245
T -0.3219263  1.2630350

Visualize it