Create lower triangle genetic distance matrix

Question

I have distance matrix like this

      1   2   3   4   5
A   0.1 0.2 0.3 0.5 0.6
B   0.7 0.8 0.9 1   1.1
C   1.2 1.3 1.4 1.5 1.6
D   1.7 1.8 1.9 2   2.1
E   2.2 2.3 2.4 2.5 2.6

and now I want to create lower triangle matrix like this

    1   2   3   4   5   A   B   C   D   E
1   0                                   
2   0.1 0                               
3   0.2 0.1 0                           
4   0.4 0.3 0.2 0                       
5   0.5 0.4 0.3 0.1 0                   
A   0.1 0.2 0.3 0.5 0.6 0               
B   0.7 0.8 0.9 1   1.1 0.6 0           
C   1.2 1.3 1.4 1.5 1.6 1.1 0.5 0       
D   1.7 1.8 1.9 2   2.1 1.6 1   0.5 0   
E   2.2 2.3 2.4 2.5 2.6 2.1 1.5 1   0.5 0

I just deducted distance between 2 from 1 from first table to get genetic distance between 1 and 2 (0.2 - 0.1=0.1) and like this I did for rest of the entries and I do not know doing like this is correct or not?, after doing calculation like that made lower triangle matrix. I tried like this in R

x <- read.csv("AD2.csv", head = FALSE, sep = ",")
b<-lower.tri(b, diag = FALSE)

but I am getting only TRUE and FALSE as output not like distance matrix. can any one help to solve this problem and here is link to my example data.

chinsoon12 chinsoon12 · Accepted Answer · 2018-01-30T09:14:10

You can make use of dist to calculate sub-matrices. Then use cbind and create the top and bottom half. Then rbind the 2 halves. Then set upper triangular to NA to create the desired output.

mat <- rbind(
    cbind(as.matrix(dist(tbl[1,])), tbl),
    cbind(tbl, as.matrix(dist(tbl[,1])))
)
mat[upper.tri(mat, diag=FALSE)] <- NA
mat

Hope it helps.

data:

tbl <- as.matrix(read.table(text="1   2   3   4   5
A   0.1 0.2 0.3 0.5 0.6
B   0.7 0.8 0.9 1   1.1
C   1.2 1.3 1.4 1.5 1.6
D   1.7 1.8 1.9 2   2.1
E   2.2 2.3 2.4 2.5 2.6", header=TRUE, check.names=FALSE, row.names=1))

Create lower triangle genetic distance matrix

1 Answers