fine_map: Visualize haplotype switches for fine mapping

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Visualize haplotype switches for fine mapping

Description

Visualize haplotype switches for fine mapping

Usage

fine_map(data, haplotype, interval, trait = NULL, marker = NULL)

Arguments

data	Variable inheriting from class diallel_geno
haplotype	Name of parental haplotype
interval	2-vector with marker names
trait	Name of trait to plot (optional)
marker	Optional, marker to indicate with dashed line

Details

Function returns graphic for all individuals with a haplotype switch (defined as change in dosage from 0 to \geq 1 or vice versa) for haplotype within interval. If trait is included, the trait values for each individual are displayed on the right side. The function requires map positions in bp to be included in data.

Value

ggplot2 variable

Examples

## Not run: 
  fine_map(data = diallel_example, 
           haplotype = "W6511-1R.2", 
           interval = c("solcap_snp_c2_40766","solcap_snp_c1_15225"))
  
  fine_map(data = diallel_example, 
           haplotype = "W6511-1R.2", 
           interval = c("solcap_snp_c2_40766","solcap_snp_c1_15225"),
           marker = "solcap_snp_c2_25522")
  
## End(Not run)

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