qtlhot (version 1.0.4)

hotsize: Hotspot size routines.

Description

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

Usage

hotsize(hotobject, …)
# S3 method for scanone
hotsize(hotobject, lod.thr = NULL, drop.lod = 1.5, …)
# S3 method for highlod
hotsize(hotobject, lod.thr = NULL, window = NULL,
  quant.level = NULL, …)
# S3 method for hotsize
print(x, …)
# S3 method for hotsize
summary(object, …)
# S3 method for 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.

See Also

highlod, hotperm

Examples

# NOT RUN {
example(highlod)
hots1 <- hotsize(high1)
summary(hots1)
plot(hots1)
# }