summary.vhicaimage: Provides a data.frame that nicely displays the information...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/summary.vhicaimage.R

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

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## 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 <lerouzic@legs.cnrs-gif.fr> 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

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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)

vhica documentation built on March 2, 2020, 5:07 p.m.