CODEWITHSUNDEEP
rtreephylogenyape
BMT
BMT

Reputation: 65

Creating a vector using tree$edge rows

I would like to create a vector of names using the tree$edge rows of a phylogenetic tree. How can I construct this vector? Example:

tree$edge # object
     [,1] [,2]
  [1,]   82   83
  [2,]   83   84
  [3,]   84   85
  [4,]   85   86
  [5,]   86   87
  [6,]   87   88
  [7,]   88   89
  [8,]   89   90
  [9,]   90   91
 [10,]   91    1
 [11,]   91   92
 [12,]   92    2
 [13,]   92   93
 [14,]   93   94
 [15,]   94    3
 [16,]   94    4
 [17,]   93   95
 [18,]   95   96
 [19,]   96    5
 [20,]   96    6

I would like to create a vector (that I call "vector_names) that each element is one of the rows of tree$edge. I can do this doing row by row:

vector_names = c(paste(tree$edge[1,1],tree$edge[1,2], sep = "_"), 
               paste(tree$edge[2,1],tree$edge[2,2], sep = "_"),
               paste(tree$edge[3,1],tree$edge[3,2], sep = "_"),
                and so on until last row ....)

The result will be:

vector_names = 82_83, 83_84, 84_85, 85_86, etc.

but is a long table with 161 rows and I would like to know if there is a faster way to produce the vector_names above.

Upvotes: 0

Views: 85

Answers (3)

Martin Smith
Martin Smith

Reputation: 4077

The simplest and most computationally efficient approach would be apply(tree3$edge, 1, paste0, collapse = '_')

Upvotes: 0

ThomasIsCoding
ThomasIsCoding

Reputation: 101628

Perhaps you can try fread from data.table like below

tree <- as.matrix(fread(text = paste0(paste0(vector_names, "\t")), sep = "_"))

or read.table from base R

tree <- as.matrix(read.table(text = paste0(paste0(vector_names, "\t")), sep = "_"))

which gives

     V1 V2
[1,] 82 83
[2,] 83 84
[3,] 84 85
[4,] 85 86

Update

If you want to get vector_names from tree, you can try

> do.call(paste, c(data.frame(tree), sep = "-"))
[1] "82-83" "83-84" "84-85" "85-86"

Data

vector_names <- c("82_83", "83_84", "84_85", "85_86")

tree <- structure(c(82, 83, 84, 85, 83, 84, 85, 86), .Dim = c(4L, 2L))

Upvotes: 0

akrun
akrun

Reputation: 887173

We can use strsplit to split by _ and then rbind the list elements

do.call(rbind, lapply(strsplit(vector_names, "_"), as.numeric))

data

vector_names <- c("82_83", "83_84", "84_85", "85_86")

Upvotes: 0

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