highlod: Pull high LOD values with chr and pos.

Description

Pull high LOD values with chr and pos.

Usage

highlod(scans, lod.thr = 0, drop.lod = 1.5,
  extend = TRUE, restrict.lod = FALSE, …)
pull.highlod(object, chr, pos, …)
# S3 method for highlod
print(x, …)
# S3 method for highlod
summary(object, …)
# S3 method for highlod
plot(x, …, quant.level = NULL, sliding = FALSE)
# S3 method for highlod
max(x, lod.thr = NULL, window = NULL, quant.level = NULL, …)
# S3 method for highlod
quantile(x, probs = NULL, lod.thr = NULL, n.quant,
  n.pheno, max.quantile = TRUE, …)

Arguments

scans

object of class scanone

lod.thr

LOD threshold

drop.lod

LOD drop from max to keep for support intervals

extend

extend support interval just past drop.lod; matches behavior of lodint when TRUE

restrict.lod

restrict to loci above LOD threshold if TRUE; matches behavior of lodint when FALSE (default)

chr

chromosome identifier

pos

position, or range of positions, in cM

x,object

object of class highlod

probs

probability levels for quantiles (should be > 0.5)

n.quant

maximum of s.quant

n.pheno

number of phenotypes considered

max.quantile

return only quantiles of max LOD across genome if TRUE

window

size of window for smoothing hotspot size

quant.level

vector of LOD levels for 1 up to length(quant.level) size hotspots

sliding

plot as sliding hotspot if TRUE

…

arguments passed along

Value

Data frame with

row

row number in scanone object

phenos

phenotype column number

lod

LOD score for phenotype at locus indicated by row

Details

The highlod condenses a scanone object to the peaks above a lod.thr and/or within drop.lod of such peaks. The pull.highlod pulls out the entries at a particular genomic location or interval of locations. Summary, print, plot, max and quantile methods provide ways to examine a highlod object.

Examples

Run this code

# NOT RUN {
example(include.hotspots)
scan1 <- scanone(cross1, pheno.col = 1:1000, method = "hk")
high1 <- highlod(scan1, lod.thr = 2.11, drop.lod = 1.5)
pull.highlod(high1, chr = 2, pos = 24)
summary(high1, lod.thr = 2.44)
max(high1, lod.thr = seq(2.11, 3.11, by = .1))
# }