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 = "",
  ...
)
# S3 method for hotsize
max(x, ...)

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.

Arguments

hotobject: object of class scanone or highlod
...: arguments passed along to scanone methods
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

Author

Brian S Yandell and Elias Chaibub Neto

Examples

Run this code


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