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Import LD decay results

import_ld_decay.Rd

Import LD decay summaries into a typed tidy object for use with plot_ld_decay() or ggpop() + geom_ld_decay(). PopLDdecay *.stat.gz and *.bin.gz files are read directly. PLINK pairwise *.ld files are summarized into distance bins.

Usage

import_ld_decay(
  dir = NULL,
  ...,
  type = c("poplddecay", "plink", "auto"),
  pop = NULL,
  pop_group = NULL,
  method = c("MeanBin", "none", "MedianBin", "PercentileBin"),
  bin1 = 10,
  bin2 = 100,
  breakpoint = 100,
  percent = 0.5,
  bin_size = NULL
)

Arguments

dir

Directory containing LD decay result files.

...

Optional named file paths. Relative paths are resolved inside dir.

type

Input type. Supports "poplddecay" and "plink".

pop

Optional sample or group labels for input files. A scalar is recycled across files; a vector is matched to file order.

pop_group

Optional population group table or path to the standard two-column sample pop file. File labels are matched through sample.

method

Binning method for PopLDdecay summaries and PLINK pairwise LD tables. "MeanBin" matches the common PopLDdecay summary plot; "MedianBin" and "PercentileBin" use pair-count weighted quantiles.

bin1

Short-distance bin width in base pairs.

bin2

Long-distance bin width in base pairs.

breakpoint

Distance threshold that switches from bin1 to bin2.

percent

Percentile used by "PercentileBin".

bin_size

Legacy alias for a single bin width. When supplied, method is treated as "MeanBin" and both bin widths use the same size.

Value

A ggpop_ld_decay tidy S3 data frame with standardized columns including dist, dist_kb, r2, pop, and n_pairs.

Details

Population grouping follows the package-wide convention: pop_group is the standard two-column sample pop table used by PCA and admixture workflows. LD decay file labels are stored as sample_id; when pop_group is supplied, matching labels are mapped to pop. The plotting helpers use the mapped population label for colour. Point and line styles keep the imported summaries; the fitted style summarizes mapped rows by population before drawing fitted curves.

Examples

ld_dir <- system.file("extdata", "ld_decay", "PopLDdecay_grouped", package = "ggPopi")
groups <- system.file("extdata", "pop_group.txt", package = "ggPopi")
ld <- import_ld_decay(ld_dir, type = "poplddecay", pop_group = groups)
#> Error: `dir` must point to an existing directory.
ld |> plot_ld_decay(style = "point")
#> Error: object 'ld' not found
ld |> plot_ld_decay(style = "line")
#> Error: object 'ld' not found
ld |> plot_ld_decay(style = "fit")
#> Error: object 'ld' not found