cnPanel: Lattice panel function for plotting raw copy number estimates...

In rscharpf/crlmmCompendium: This package contains the compendium for copy number estimation with the crlmm package

Description

Lattice panel function for plotting raw copy number estimates versus physical position. The segmentation results are overplotted as line segments. Hidden states from a hidden markov model are plotted just beneath the 0 y-coordinate.

Usage

cnPanel(x, y, ..., pch.cols, gt, cbs.segs, hmm.segs, shades, subscripts, add.ideogram = TRUE)

Arguments

x	physical position (integer vector) passed to panel.xyplot
y	raw copy number estimates (numerical vector) passed to panel.xyplot
...	additional arguments to panel.xyplot
pch.cols	color of plotting symbols to distinguish heterozygous genotypes (AB) from homozygous genotypes (AA or BB)
gt	integer vector indicating the diallelic genotype calls (1=AA, 2=AB, 3=BB). Use 'NA' for nonpolymorphic loci.
cbs.segs	RangedData object containing start and stop positions (unit is basepairs) and the segment mean labeled as 'seg.mean'
hmm.segs	Results from HMM implemented in the VanillaICE package
shades	Shades for coloring the hidden states
subscripts	additional arguments for panel.xyplot
add.ideogram	whether to add the ideogram at the top (y-coordinates are 5.6 - 5.9).

Value

Nothing

Author(s)

R. Scharpf

See Also

panel.xyplot

rscharpf/crlmmCompendium documentation built on May 28, 2019, 3:31 a.m.