Indexing aphylo objects
# S3 method for aphylo
[(x, i, j, drop = FALSE)
# S3 method for aphylo
[(x, i, j) <- valueAn object of class aphylo.
Integer vector. Indices of genes or functions.
Logical scalar. When TRUE, the function returns a matrix of
annotations. Otherwise an object of class aphylo.
Integer vector. Replacing values, can be either c(0, 1, 9, NA).
When indexing with i: A data frame with the annotations of the
selected genes.
When only indexing with j (drop = FALSE): An aphylo object with the selected sets of
annotations.
When only indexing with j (drop = TRUE): A data.frame with the selected
annotations.
When indexing on both i and j: A data.frame with the selected genes and annotations.
The subsetting method allows selecting one or more annotations from
the aphylo object. Whenever i is specified, then aphylo returns the corresponding
annotations.
set.seed(12312)
atree <- raphylo(50, P = 4)
atree[1:10,]
#> fun0000 fun0001 fun0002 fun0003
#> 1 1 1 0 1
#> 2 1 1 1 1
#> 3 1 0 0 0
#> 4 1 0 1 1
#> 5 0 1 1 1
#> 6 1 1 1 1
#> 7 1 1 1 1
#> 8 0 0 0 1
#> 9 1 1 1 1
#> 10 0 1 1 1
atree[,2:3]
#>
#> Phylogenetic tree with 50 tips and 49 internal nodes.
#>
#> Tip labels:
#> 1, 2, 3, 4, 5, 6, ...
#> Node labels:
#> 51, 52, 53, 54, 55, 56, ...
#>
#> Rooted; no branch lengths.
#>
#> Tip (leafs) annotations:
#> fun0001 fun0002
#> 1 1 0
#> 2 1 1
#> 3 0 0
#> 4 0 1
#> 5 1 1
#> 6 1 1
#>
#> ...(44 obs. omitted)...
#>
#>
#> Internal node annotations:
#> fun0001 fun0002
#> 1 1 0
#> 2 1 0
#> 3 1 0
#> 4 1 1
#> 5 1 1
#> 6 0 1
#>
#> ...(43 obs. omitted)...
#>
atree[, 2:3, drop = TRUE]
#> fun0001 fun0002
#> 1 1 0
#> 2 1 1
#> 3 0 0
#> 4 0 1
#> 5 1 1
#> 6 1 1
#> 7 1 1
#> 8 0 0
#> 9 1 1
#> 10 1 1
#> 11 1 1
#> 12 1 0
#> 13 1 1
#> 14 1 0
#> 15 1 0
#> 16 1 1
#> 17 1 0
#> 18 1 0
#> 19 1 1
#> 20 1 1
#> 21 1 0
#> 22 1 1
#> 23 0 0
#> 24 0 0
#> 25 1 1
#> 26 1 0
#> 27 1 1
#> 28 0 1
#> 29 1 0
#> 30 1 0
#> 31 1 1
#> 32 1 0
#> 33 1 1
#> 34 1 0
#> 35 0 1
#> 36 1 1
#> 37 1 1
#> 38 1 0
#> 39 0 1
#> 40 1 0
#> 41 1 1
#> 42 1 1
#> 43 0 1
#> 44 1 0
#> 45 1 1
#> 46 0 1
#> 47 1 1
#> 48 1 1
#> 49 1 1
#> 50 1 0
#> 1 1 0
#> 2 1 0
#> 3 1 0
#> 4 1 1
#> 5 1 1
#> 6 0 1
#> 7 1 1
#> 8 1 1
#> 9 1 1
#> 10 1 0
#> 11 1 0
#> 12 1 1
#> 13 1 1
#> 14 1 1
#> 15 1 0
#> 16 1 1
#> 17 1 1
#> 18 0 1
#> 19 1 1
#> 20 1 0
#> 21 0 1
#> 22 1 0
#> 23 0 1
#> 24 1 0
#> 25 1 1
#> 26 1 1
#> 27 1 1
#> 28 1 1
#> 29 1 1
#> 30 1 1
#> 31 1 1
#> 32 1 0
#> 33 1 1
#> 34 1 0
#> 35 1 1
#> 36 1 0
#> 37 1 0
#> 38 0 0
#> 39 1 1
#> 40 1 0
#> 41 1 1
#> 42 0 0
#> 43 0 1
#> 44 0 0
#> 45 0 1
#> 46 1 0
#> 47 1 0
#> 48 1 1
#> 49 1 1
atree[1:10, 2:3]
#> fun0001 fun0002
#> 1 1 0
#> 2 1 1
#> 3 0 0
#> 4 0 1
#> 5 1 1
#> 6 1 1
#> 7 1 1
#> 8 0 0
#> 9 1 1
#> 10 1 1