slidingWindow {spider} | R Documentation |
Create windows along an alignment
Description
Creates windows of a specified width along a DNA alignment.
Usage
slidingWindow(DNAbin, width, interval = 1)
Arguments
DNAbin |
A DNA alignment of class ‘DNAbin’. |
width |
Width of each window. |
interval |
Numeric or option of |
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
.
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 retreived with attr(x,
"window")
.
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
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")