print.LD: Textual and graphical display of linkage disequilibrium (LD)...

In kindlychung/genetics: Population Genetics

Description

Textual and graphical display of linkage disequilibrium (LD) objects

Usage

## S3 method for class 'LD'
print(x, digits = getOption("digits"), ...)
## S3 method for class 'LD.data.frame'
print(x, ...)

## S3 method for class 'data.frame'
summary.LD(object, digits = getOption("digits"),
                      which = c("D", "D'", "r", "X^2", "P-value", "n", " "),
                      rowsep, show.all = FALSE, ...)
## S3 method for class 'summary.LD.data.frame'
print(x, digits = getOption("digits"), ...)

## S3 method for class 'LD.data.frame'
plot(x,digits=3, colorcut=c(0,0.01, 0.025, 0.5, 0.1, 1),
                   colors=heat.colors(length(colorcut)), textcol="black",
                   marker, which="D'", distance,  ...)


LDtable(x, colorcut=c(0,0.01, 0.025, 0.5, 0.1, 1),
        colors=heat.colors(length(colorcut)), textcol="black",
        digits=3, show.all=FALSE, which=c("D", "D'", "r", "X^2",
        "P-value", "n"), colorize="P-value", cex, ...)

LDplot(x, digits=3, marker, distance, which=c("D", "D'", "r", "X^2",
       "P-value", "n", " "), ... )

Arguments

x,object	LD or LD.data.frame object
digits	Number of significant digits to display
which	Name(s) of LD information items to be displayed
rowsep	Separator between rows of data, use NULL for no separator.
colorcut	P-value cutoffs points for colorizing LDtable
colors	Colors for each P-value cutoff given in colorcut for LDtable
textcol	Color for text labels for LDtable
marker	Marker used as 'comparator' on LDplot. If omitted separate lines for each marker will be displayed
distance	Marker location, used for locating of markers on LDplot.
show.all	If TRUE, show all rows/columns of matrix. Otherwise omit completely blank rows/columns.
colorize	LD parameter used for determining table cell colors
cex	Scaling factor for table text. If absent, text will be scaled to fit within the table cells.
...	Optional arguments (plot.LD.data.frame passes these to LDtable and LDplot)

Value

None.

Author(s)

Gregory R. Warnes [e-mail]

See Also

LD, genotype, HWE.test

Examples

g1 <- genotype( c('T/A',    NA, 'T/T',    NA, 'T/A',    NA, 'T/T', 'T/A',
                  'T/T', 'T/T', 'T/A', 'A/A', 'T/T', 'T/A', 'T/A', 'T/T',
                     NA, 'T/A', 'T/A',   NA) )

g2 <- genotype( c('C/A', 'C/A', 'C/C', 'C/A', 'C/C', 'C/A', 'C/A', 'C/A',
                  'C/A', 'C/C', 'C/A', 'A/A', 'C/A', 'A/A', 'C/A', 'C/C',
                  'C/A', 'C/A', 'C/A', 'A/A') )


g3 <- genotype( c('T/A', 'T/A', 'T/T', 'T/A', 'T/T', 'T/A', 'T/A', 'T/A',
                  'T/A', 'T/T', 'T/A', 'T/T', 'T/A', 'T/A', 'T/A', 'T/T',
                  'T/A', 'T/A', 'T/A', 'T/T') )
data <- makeGenotypes(data.frame(g1,g2,g3))

# Compute & display  LD for one marker pair
ld <- LD(g1,g2)
print(ld)

# Compute LD table for all 3 genotypes
ldt <- LD(data)

# display the results
print(ldt)                               # textual display
LDtable(ldt)                            # graphical color-coded table
LDplot(ldt, distance=c(124, 834, 927))  # LD plot vs distance

# more markers makes prettier plots!
data <- list()
nobs <- 1000
ngene <- 20
s <- seq(0,1,length=ngene)
a1 <- a2 <- matrix("", nrow=nobs, ncol=ngene)
for(i in 1:length(s) )
{

  rallele <- function(p) sample( c("A","T"), 1, p=c(p, 1-p))

  if(i==1)
    {
      a1[,i] <- sample( c("A","T"), 1000, p=c(0.5,0.5), replace=TRUE)
      a2[,i] <- sample( c("A","T"), 1000, p=c(0.5,0.5), replace=TRUE)
    }
  else
    {
      p1 <- pmax( pmin( 0.25 + s[i] * as.numeric(a1[,i-1]=="A"),1 ), 0 )
      p2 <- pmax( pmin( 0.25 + s[i] * as.numeric(a2[,i-1]=="A"),1 ), 0 )
      a1[,i] <- sapply(p1, rallele )
      a2[,i] <- sapply(p2, rallele )
    }

  data[[paste("G",i,sep="")]] <- genotype(a1[,i],a2[,i])
}
data <- data.frame(data)
data <- makeGenotypes(data)

ldt <- LD(data)
plot(ldt, digits=2, marker=19) # do LDtable & LDplot on in a single
                               # graphics window

kindlychung/genetics documentation built on May 20, 2019, 9:58 a.m.