hotspot: Hotspots for phenotypes

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

Hotspots for phenotypes

Description

Count hotspots by pheno_group and pheno_type.

Usage

hotspot(map, peaks, peak_window = 1, minLOD = 5.5)

Arguments

map	list of genetic maps
peaks	data frame of peak information
peak_window	half-width of peak window in Mbp
minLOD	minimum LOD to include in count

Value

object of class hotspot as list of scan1 and map objects.

Author(s)

Brian S Yandell, [e-mail]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- qtl2::read_cross2(file.path(dirpath, "DOex.zip"))
DOex <- subset(DOex, chr = "2")

# Calculate genotype and allele probabilities
pr <- qtl2::calc_genoprob(DOex, error_prob=0.002)

# Summary of coefficients at scan peak
scan_pr <- qtl2::scan1(pr, DOex$pheno)
peaks <- summary(scan_pr, DOex$pmap)

hotspot(DOex$pmap, peaks)

# Select Sex and Cohort columns of covariates
analyses_tbl <- data.frame(pheno = "OF_immobile_pct", Sex = TRUE, Cohort = TRUE)

# Get hotspot (only one phenotype here).
out <- hotspot(DOex$pmap, peaks)
summary(out)

byandell/qtl2shiny documentation built on Nov. 9, 2023, 7:58 p.m.