spider (version 1.5.1)

slidingWindow: Create windows along an alignment

Description

Creates windows of a specified width along a DNA alignment.

Usage

slidingWindow(DNAbin, width, interval = 1)

Value

A list of `DNAbin' objects, with each alignment being width

bases in length. The list has length of the DNA alignment minus the width. The positions covered by each window can be retrieved with attr(x, "window").

Arguments

DNAbin

A DNA alignment of class `DNAbin'.

width

Width of each window.

interval

Numeric or option of "codons". This sets interval between windows. Default of 1. Setting the option to "codons" gives an interval of 3.

Author

Samuel Brown <[e-mail]>

Details

Sliding window analyses are often used to determine the variability along sequences. This can be useful for investigating whether there is evidence for recombination, developing shorter genetic markers, or for determining variation within a gene.

Analyses can be conducted on each window using lapply.

See Also

lapply, slideAnalyses, slideBoxplots.

Examples

data(woodmouse)
woodmouse <- woodmouse[,1:20]
win1 <- slidingWindow(woodmouse, width = 10)
length(win1)

win2 <- slidingWindow(woodmouse, width = 10, interval = 2)
length(win2)

win3 <- slidingWindow(woodmouse, width = 10, interval = "codons")
length(win3)

win4 <- slidingWindow(woodmouse, width = 15)
length(win4)
attr(win4[[1]], "window")
attr(win4[[2]], "window")