summary.vhicaimage {vhica}

Provides a data.frame that nicely displays the information returned by image.vhica.

Description

The image.vhica routine displays visually the statistical support for horizontal transfers, and can return an object of class vhicaimage. The current summary method reorganizes this object into a dataframe that can be displayed or reused in further analysis.

Usage

## S3 method for class 'vhicaimage'
summary(object, divrate=NA, p.thresh=1, ...)

Arguments

object

An object of class vhicaimage, created by image.vhica.

divrate

Optional divergence rate (in neutral substitutions per Myr).

p.thresh

Optional p-value threshold. By default, all data is returned.

...

Additional options for summary (unused).

Value

The resulting data.frame has 4 or 5 columns. The two first columns are sp1 and sp2, the two species between which the horizontal transfer is tested, in an arbitrary order. The column p.value contains the p-value calculated as in image.vhica (including the possible correction for multiple testing). The dS column is a copy of the corresponding divergence from the original data. The last, optional column Time(Mya) is a molecular clock estimate of the time of divergence between the two sequences, based on the divergence rate (when provided).

Author(s)

Implementation: Arnaud Le Rouzic <[e-mail]> and Gabriel Wallau
Scientists who designed the method: Gabriel Wallau, Aurélie Hua-Van, Arnaud Le~Rouzic.

References

Gabriel Luz Wallau, Arnaud Le Rouzic, Pierre Capy, Elgion Loreto, Aurélie Hua-Van. VHICA: A new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila. Molecular biology and evolution 33 (4), 1094-1109.

See Also

read.vhica, image.vhica

Examples

file.cb <- system.file("extdata", "mini-cbias.txt", package="vhica")
file.div <- system.file("extdata", "mini-div.txt", package="vhica")
file.tree <- if(require("ape")) system.file("extdata", "phylo.nwk", package="vhica") else NULL
vc <- read.vhica(cb.filename=file.cb, div.filename=file.div)
plot(vc, "dere", "dana")
im <- image(vc, "mellifera:6", treefile=file.tree, skip.void=TRUE)
summary(im)