Subset a TCRrep object by row indices

Subsets a TCRrep by clonotype indices. Filters clone_df and all associated distance matrices simultaneously. KNN matrices and meta-clonotypes are cleared since they reference the original indexing.

Usage

# S4 method for class 'TCRrep,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

Arguments

x

A TCRrep object.

i

Row indices: logical, integer, or character (rownames).

j

Ignored.

...

Ignored.

drop

Ignored.

Value

A new TCRrep object with the selected clonotypes.

Examples

# \donttest{
data(dash)
rep <- TCRrep(dash, organism = "mouse", compute_distances = TRUE)
#> deduplicate: 1924 -> 1888 clones
pa <- rep[rep@clone_df$epitope == "PA", ]
pa
#> TCRrep object: 321 clonotypes
#>   organism: mouse
#>   chains: AB
#>   metric: tcrdist
#>   distances: paired(dense)
# }