highlod: Pull high LOD values with chr and pos.

In qtlhot: Inference for QTL Hotspots

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 class 'highlod'
print(x, ...)
## S3 method for class 'highlod'
summary(object, ...)
## S3 method for class 'highlod'
plot(x, ..., quant.level = NULL, sliding = FALSE)
## S3 method for class 'highlod'
max(x, lod.thr = NULL, window = NULL, quant.level = NULL, ...)
## S3 method for class '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

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.

Value

Data frame with

row	row number in scanone object
phenos	phenotype column number
lod	LOD score for phenotype at locus indicated by row

Author(s)

Brian S Yandell and Elias Chaibub Neto

See Also

highlod, hotperm

Examples

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))

qtlhot documentation built on May 2, 2019, 11:06 a.m.