calc_lod_scores: Perform a LOD scan.

In churchill-lab/qtl2api: QTL2 API Library

Perform a LOD scan.

Description

Perform a LOD scan.

Usage

calc_lod_scores(
  dataset,
  id,
  intcovar = NULL,
  cores = 0,
  filter_threshold = 6,
  filter_peak_drop = Inf,
  filter_thresholdX = NULL,
  filter_peak_dropX = NULL,
  scan1_output = FALSE
)

Arguments

dataset	The dataset object.
id	The unique id in the dataset.
intcovar	The interactive covariate.
cores	Number of cores to use (0 = ALL).
filter_threshold	If set, qtl2::find_peaks is used.
filter_peak_drop	If set, qtl2::find_peaks is used.
filter_thresholdX	If set, qtl2::find_peaks is used.
filter_peak_dropX	If set, qtl2::find_peaks is used.
scan1_output	If 'TRUE', original 'qtl2::scan1' data is included.

Value

a 'list' with the following elements:

• lod_peaks - 'tibble' of LOD peaks

• lod_scores - 'tibble' with the following columns: id, chr, pos, lod

• scan1 - 'qtl2::scan1' output

churchill-lab/qtl2api documentation built on April 17, 2025, 3:27 a.m.