Count chain rows in ImmunData¶

Description¶

Use count() to find how many chain rows are stored in an ImmunData object.

Use this method for a quick check of dataset size. The unit counted is one retained chain row. Each retained cell with a paired receptor usually contributes two rows, one for each chain. The same receptor can therefore contribute two rows for every cell carrying it. For bulk data with an abundance column, this method counts table rows rather than the summed sequence abundance.

The function returns a one-row duckplyr table. The original object is not changed.

Usage¶

## S3 method for class 'ImmunData'
count(x, ..., wt = NULL, sort = FALSE, name = NULL)

Arguments¶

x An ImmunData object.

… Additional arguments. Accepted for compatibility with dplyr::count(), but currently ignored.

wt Any value or NULL. Accepted for compatibility with dplyr::count(), but currently ignored.

sort A logical value. Accepted for compatibility with dplyr::count(), but currently ignored.

name A character string or NULL. Accepted for compatibility with dplyr::count(), but currently ignored. The result column is always named n.

Details¶

This method currently provides only the total row count. The grouping, weighting, sorting, and result-name arguments of dplyr::count() are accepted for method compatibility but are not applied.

The calculation runs on the duckplyr annotation table and can remain in DuckDB. Use dplyr::pull() or dplyr::collect() to bring the small result into R.

Value¶

A one-row duckplyr table with an integer column named n. This value is the number of rows in the chain-level annotation table.

Examples¶

library("immundata")

library(immundata)
library(dplyr)

options(immundata.verbose = FALSE)
idata <- get_test_idata()

idata |> count()

#> # A duckplyr data frame: 1 variable
#>       n
#>   <int>
#> 1  1902

# Expected result:
#      n
#   1902

# The result means that the object contains 1,902 retained chain rows.
# It does not mean that it contains 1,902 unique receptors.