xypanelBaf {SNPchip} | R Documentation |
Panel function for plotting copy number and B allele frequencies for a genomic interval.
xypanelBaf(x, y, gt, baf, is.snp, range, col.hom = "grey20", fill.hom = "lightblue", col.het = "grey20", fill.het = "salmon", col.np = "grey20", fill.np = "grey60", show.state = TRUE, state.cex = 1, col.state = "blue", ..., subscripts)
x |
physical position in basepairs |
y |
total copy number (relative or absolute) |
gt |
Genotypes coded as integers (1=AA, 2=AB, 3=BB). This is optional. If provided one can color code the plotting symbols by the genotype. |
baf |
B allele frequencies. |
is.snp |
Logical. Indicator of whether the marker hybridized to a known SNP or a nonpolymorphic region of the genome. |
range |
A |
col.hom |
Color to use for homozygous genotypes. |
fill.hom |
Fill color to use for homozygous genotypes. |
col.het |
Color to use for heterozygous genotypes. |
fill.het |
Fill color to use for heterozygous genotypes. |
col.np |
Color to use for nonpolymorphic markers |
fill.np |
Fill color for nonpolymorphic markers. |
show.state |
Logical indicating whether to display the copy number state for a |
state.cex |
Size of the font for displaying the HMM state. Ignored if
|
col.state |
Color for displaying the state. |
... |
Additional arguments passed to |
subscripts |
See |
Function for plotting B allele frequencing and copy number on a
trellis display. Intended to be passed to the panel argument of the
function xyplotLrrBaf
and should not be called directly by
the user.
R.Scharpf