print.trioFS {trio} | R Documentation

## Printing and plotting of a trioFS object

### Description

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

### Usage

    ## S3 method for class 'trioFS'
    print(x, topX = 5, show.prop = TRUE, coded = FALSE, digits = 2, ...)

    ## S3 method for class 'trioFS'
    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 `print`ed or (if `force.topX = FALSE`) `plot`ted.
`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 `plot`ted, 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 `print`ed 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 `plot`ted. If `FALSE` (default) all interactions up to the `topX`th most important one and all interactions having the same importance as the `topX`th most important one are `plot`ted.
`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.

### Author(s)

Holger Schwender, holger.schwender@udo.edu

### 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)

[Package trio version 3.20.0 Index]