Generate Blueprint Copy Number Profiles

Source: R/pattern_extraction.R

This function generates copy number (CN) profiles for clones based on their events and a genome-wide window vector. It initializes baseline CN profiles for paternal and maternal haplotypes and updates them according to the events (e.g., copy number changes, whole genome duplications) associated with each clone. The function handles both whole chromosome events and specific region events.

generate_blueprint_cn_profiles(
  clone_events,
  genome_window_vector,
  segment_info
)

Arguments

clone_events

A named list of data frames, where each data frame contains events for a clone:

  • event_type: Type of event (e.g., "WGD" for whole genome duplication)

  • region_name: Region identifier or chromosome name

  • CN_change: Copy number change value

  • haplotype: "maternal" or "paternal"

genome_window_vector

A character vector of window identifiers in format "chr_start_end"

segment_info

A data frame containing segment information:

  • region_name: Region identifier

  • chrom: Chromosome name

  • start: Start position

  • end: End position

Value

A list with two elements ("maternal" and "paternal"), each containing a data frame where:

  • Rows represent clones

  • Columns represent genomic windows

  • Values represent copy numbers

Details

The function processes events in these steps:

  1. Initializes baseline copy numbers (1 for all regions)

  2. For each clone and its events:

    • Handles WGD by doubling all copy numbers

    • Processes chromosome-wide events if region matches "chr0-9XY+"

    • Updates specific regions based on segment information

    • Applies copy number changes progressively

  3. Maintains separate profiles for maternal and paternal haplotypes

Note

  • Copy numbers cannot go below 0

  • WGD events affect all regions simultaneously

  • Chromosome-wide events are detected by regex pattern

Examples

if (FALSE) { # \dontrun{
clone_events <- list(
  clone1 = data.frame(
    event_type = c("CN", "WGD"),
    region_name = c("chr1_p", "genome"),
    CN_change = c(1, 0),
    haplotype = c("maternal", "maternal")
  ),
  clone2 = data.frame(...)
)
genome_windows <- c("chr1_0_1000000", "chr1_1000000_2000000")
segments <- data.frame(
  region_name = "chr1_p",
  chrom = "chr1",
  start = 0,
  end = 1000000
)
profiles <- generate_blueprint_cn_profiles(clone_events, genome_windows, segments)
} # }