Calculate clone barcode with at least x number of cells

This function calculates the number of clones with at least a specified number of cells. Clones with fewer cells than the threshold are excluded from the count.

count_retained_clones(count_data, thresholds, count_column, grouping_col = NA)

Arguments

count_data

A data.table where each row corresponds to a clone barcode.

thresholds

A numeric vector listing the minimum cell counts required for a clone to be included in the count. The calculation will be applied for each value in the vector.

count_column

A character indicating the column storing the count of the clone barcodes.

grouping_col

A character string, default NA. If provided, the function repeats the calculation for each subsets of `count_data` defined by this column, effectively a group-by operation.

Value

A data.table containing the counts of clones that meet or exceed the specified threshold.

Examples

library(data.table)

toy_clone_counts <- data.table(
sample_name = c(rep("test1", 2), rep("test2", 3)),
clone_barcode = c("A", "B", "C", "D", "E"),
read_count = c(1, 5, 10, 15, 20)
)

count_retained_clones(
  count_data = toy_clone_counts,
  thresholds = c(2, 10),
  count_column = "read_count",
  grouping_col = "sample_name"
)
#>    sample_name at_least_2_cells at_least_10_cells
#> 1:       test1                1                 0
#> 2:       test2                3                 3