haplo_freq: Haplotype frequencies

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Haplotype frequencies

Description

Plots the frequency of individuals with haplotype dosage above a threshold

Usage

haplo_freq(
  data,
  haplotypes,
  dosage,
  id = NULL,
  position = "cM",
  chrom = NULL,
  markers = NULL
)

Arguments

data	Variable inheriting from class diallel_geno
haplotypes	Names of haplotypes
dosage	Dosage threshold
id	Vector of id names (default is entire population)
position	Either "cM" (default) or "bp" for plotting
chrom	Names of chromosomes (default is all)
markers	Optional, markers to indicate with dashed line. Only available when plotting a single chromosome.

Details

Useful for visualizing selection in selfed populations. For multiple chromosomes, each haplotype is shown in its own panel using facet_wrap. For one chromosome, the haplotypes are shown on the same set of axes.

Value

List containing

result

Data frame with the map and frequency

plot

ggplot object

jendelman/diaQTL documentation built on Jan. 27, 2024, 6:39 a.m.