plot.LD {GeneticsBase}R Documentation

Textual and graphical display of linkage disequilibrium (LD) objects

Description

Textual and graphical display of linkage disequilibrium (LD) objects

Usage

plot(x, y, ...)
plot.LD (x, y=NULL, cex, ...)
LDView(LdMat,
       SNPloc=NULL,
       is.triangle=TRUE,
       SNPnames=NULL,
       cexSNPnames=0.2+1/log10(nrow(LdMat)),
       margins=c(6,2,3,6),
       main=NULL,
       barCol=rainbow(256,start=0,end=1/6 ),
       widths=c(10,10),
       heights=c(1,10),
       ...)



Arguments

x LD or LDband object
y currently ignored
cex Scaling factor for table text. If absent, text will be scaled to fit within the table cells.
LdMat matrix of pair-wise LD measures
SNPloc SNP locations
is.triangle indicate if 'LdMat' is a lower triangle matrix or not. if 'LdMat' is an upper triangle, then the user has to transpose it before calling the function 'LDView'.
SNPnames labels for SNPs
cexSNPnames font size for SNPs labels
margins margins for heatmap
main title for the plot
barCol specify the color scheme
widths The plot is split into two parts – upper part and lower part 'widths' specifies the widths of the two parts
heights The plot is split into two parts – upper part and lower part 'heights' specifies the heights of the two parts
... Optional arguments (plot.LD.data.frame passes these to LDtable and LDplot) and other parameters for the function 'image'

Details

LDtable generates a graphical matrix of LD coefficients. It attempts to properly set the font size so that the estimated values fit into the boxes. It also colorized the boxes to whether the estimates are significantly different from no linkage.

LDplot generates a plot of the LD coeffients across markers. By default it will overlay plots for LD against all markers. LD against a specific subset of markers can be obtained using the marker argument.

Value

SNPnames labels of the SNPs in LDView
LdMat LD matrix
SNPloc SNP positions

Author(s)

Gregory R. Warnes warnes@bst.rochester.edu

See Also

LD, geneSet, diseq

Examples


# load the data
data(CAMP)

# compute pairwise LD
ld <- LD(CAMP)

print(ld)    # text display of LD coefficents and graphical display of LD estimates

LDView(t(ld@"R^2"), SNPloc=1:8, SNPnames=CAMP@markerInfo$Name)

## LDtable(ld) # graphical display of LD estimates
## LDtable(ld, which="D'", digits=2) # graphical display of D' only 

## plot(CAMP) # two panel display


[Package GeneticsBase version 1.8.0 Index]