trio (version 3.10.0)

print.trioFS: Printing and plotting of a trioFS object

Description

Prints or plots the most important interactions found in a trioFS analysis.

Usage

"print"(x, topX = 5, show.prop = TRUE, coded = FALSE, digits = 2, ...)
"plot"(x, topX = 15, show.prop = FALSE, coded = TRUE, cex = 0.9,  pch = 16, col = 1, force.topX = FALSE, include0 = TRUE, add.v0 = TRUE,  v0.col = "grey50", main = NULL, ...)

Arguments

x

an object of class trioFS, i.e. the output of trioFS.

topX

integer specifying how many interactions should be shown. If topX is larger than the number of interactions contained in x, all the interactions are shown. Additionally to the topX most important interactions, any interaction having the same importance as the topX most important one are printed or (if force.topX = FALSE) plotted.

show.prop

should the proportions of models containing the respective interactions be added to the output (if print is used)? If the output of trioFS should be plotted, then the proportions of models can be plotted instead of the values of the importance measure by setting show.prop = TRUE.

coded

should the coded variable names be displayed? Might be useful if the actual variable names are pretty long. The coded variable name of the j-th variable is Xj.

digits

number of digits shown in the printed output.

cex

a numeric value specifying the relative size of the text and symbols.

pch

specifies the used symbol. See the help of par for details.

col

the color of the text and the symbols. See the help of par for how colors can be specified.

force.topX

if TRUE exactly topX interactions are plotted. If FALSE (default) all interactions up to the topXth most important one and all interactions having the same importance as the topXth most important one are plotted.

include0

should the $x$-axis include zero regardless whether the importances of the shown interactions are much higher than 0?

add.v0

should a vertical line be drawn at $x = 0$? Ignored if include0 = FALSE and all importances are larger than zero.

v0.col

the color of the vertical line at $x = 0$. See the help page of par for how colors can be specified.

main

character string naming the title of the plot. If NULL, a standard title is added to the plot.

...

Ignored.

See Also

trioFS

Examples

# Load the simulated data.
data(trio.data)

# Prepare the data in trio.ped1 for a trioFS analysis 
# by first calling
trio.tmp <- trio.check(dat = trio.ped1)

# and then applying
set.seed(123456)
trio.bin <- trio.prepare(trio.dat=trio.tmp, blocks=c(1,4,2,3))

# where we here assume the block structure to be
# c(1, 4, 2, 3), which means that the first LD "block"
# only consists of the first SNP, the second LD block
# consists of the following four SNPs in trio.bin,
# the third block of the following two SNPs,
# and the last block of the last three SNPs.
# set.seed() is specified to make the results reproducible.

# For the application of trioFS, some parameters of trio 
# logic regression are changed to make the following example faster.
my.control <- lrControl(start=1, end=-3, iter=1000, output=-4)

# Please note typically you should consider much more
# than 1000 iterations (usually, at least a few hundred
# thousand).

# TrioFS can then be applied to the trio data in trio.ped1 by
fs.out <- trioFS(trio.bin, control=my.control, rand=9876543)

# where we specify rand just to make the results reproducible.

# The output of trioFS can be printed by
fs.out

# By default, the five most important interactions are displayed.
# If another number of interactions, e.g., 10, should be shown,
# then this can be done by
print(fs.out, topX = 10)

# The importances can also be plotted by
plot(fs.out)