hotsize: Hotspot size routines.

In byandell/qtlhot: Inference for QTL Hotspots

Description

Determine hotspot sizes and display. Use individual threshold and quantile thresholds as provided.

Usage

hotsize(hotobject, ...)
## S3 method for class 'scanone'
hotsize(hotobject, lod.thr = NULL, drop.lod = 1.5, ...)
## S3 method for class 'highlod'
hotsize(hotobject, lod.thr = NULL, window = NULL,
  quant.level = NULL, ...)
## S3 method for class 'hotsize'
print(x, ...)
## S3 method for class 'hotsize'
summary(object, ...)
## S3 method for class 'hotsize'
plot(x, ylab = "counts", quant.axis = pretty(x$max.N),
  col = c("black", "red", "blue"), by.chr = FALSE, maps = NULL,
  title = "",...)

Arguments

hotobject	object of class scanone or highlod
lod.thr	LOD threshold
drop.lod	LOD drop from max to keep for support intervals
window	window width in cM for smoothing hotspot size; not used if 0 or NULL
quant.level	vector of LOD levels for 1 up to length(quant.level) size hotspots
x,object	object of class hotsize
ylab	label for vertical plot axis
quant.axis	hotspot sizes for quantile axis (vertical on right side of plot)
col	col of hotspot size, smoothed hotspot size, and sliding hotspot size
by.chr	separate plot by chromosome if TRUE
maps	if not NULL, list of objects of class map to use for rugs on top and bottom of plot
title	title for plot
...	arguments passed along to scanone methods

Value

hotsize methods return an object of class hotsize, which is essentially an object of class summary.scanone with additional attributes for lod.thr, window, and quant.level.

Author(s)

Brian S Yandell and Elias Chaibub Neto

See Also

highlod, hotperm

Examples

example(highlod)
hots1 <- hotsize(high1)
summary(hots1)
plot(hots1)

byandell/qtlhot documentation built on March 7, 2020, 3:25 p.m.