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Summarise LD Block Characteristics

Source: R/utils.R
summarise_blocks.Rd

Computes per-chromosome and genome-wide summary statistics for a block table returned by run_Big_LD_all_chr.

Usage

summarise_blocks(blocks)

Arguments

blocks

Data frame of LD blocks. Must contain at least start.bp, end.bp. If a CHR column is present, per-chromosome summaries are produced.

Value

A data.frame with one row per chromosome (plus one row for the genome-wide summary) and columns:

CHR

Chromosome (or "GENOME").

n_blocks

Number of blocks.

min_bp, median_bp, mean_bp, max_bp

Block size distribution in base pairs.

total_bp_covered

Sum of block sizes (bp).

Examples

# \donttest{
blocks <- data.frame(
  CHR      = c("1", "1", "2"),
  start.bp = c(1000L, 500000L, 2000L),
  end.bp   = c(80000L, 650000L, 200000L)
)
summarise_blocks(blocks)
#>      CHR n_blocks min_bp median_bp  mean_bp max_bp total_bp_covered
#> 1      1        2  79001    114501 114501.0 150001           229002
#> 2      2        1 198001    198001 198001.0 198001           198001
#> 3 GENOME        3  79001    150001 142334.3 198001           427003
# }