Creates windows of a specified width along a DNA alignment.
A DNA alignment of class ‘DNAbin’.
Width of each window.
Numeric or option of
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
A list of ‘DNAbin’ objects, with each alignment being
bases in length. The list has length of the DNA alignment minus the width.
The positions covered by each window can be retreived with
Samuel Brown <[email protected]>
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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[], "window") attr(win4[], "window")
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