Compute pairwise linkage disequilibrium between genetic markers
LD(g1, ...)# S3 method for snp
LD(g1, g2, ...)
# S3 method for setupSNP
LD(g1, SNPs, ...)
LDplot(x, digits = 3, marker, distance, which = c("D", "D'",
"r", "X^2", "P-value", "n", " "), ...)
LDtable(x, colorcut = c(0, 0.01, 0.025, 0.05, 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, ...)
None
genotype object or dataframe containing genotype objects
genotype object (ignored if g1 is a dataframe)
columns containing SNPs
LD or LD.data.frame object
Number of significant digits to display
Name(s) of LD information items to be displayed
P-value cutoffs points for colorizing LDtable
Colors for each P-value cutoff given in 'colorcut' for LDtable
Color for text labels for LDtable
Marker used as 'comparator' on LDplot. If omitted separate lines for each marker will be displayed
Marker location, used for locating of markers on LDplot.
If TRUE, show all rows/columns of matrix. Otherwise omit completely blank rows/columns.
LD parameter used for determining table cell colors
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').
functions adapted from LD, LDtable and LDplot in package genetics by Gregory Warnes et al. (warnes@bst.rochester.edu)
genetics R package by Gregory Warnes et al. (warnes@bst.rochester.edu)
setupSNP snp