Sliding.Window {VLF} | R Documentation |
Sliding Window
Description
Creates a sliding window analysis plot for the VLFs in a matrix of sequences.
Usage
Sliding.Window(VLF, seqlength, n = 30)
Arguments
VLF |
A vector of VLFs per position across the barcocde. Can be a single vector of all VLFs per positions, or can be a matrix containing singleton and shared VLFs. |
seqlength |
Length of the barcode sequence. |
n |
The number of positions to average the window across (n = 30 by default). |
Details
The argument VLF can be calculated using the function VLF.count.pos for all VLFs, or find.singles for singleton and shared VLFs.
Value
A sliding window plot for the VLFs in each position of the barcode averaged over n.
Author(s)
Taryn B. T. Athey and Paul D. McNicholas
Examples
## Not run: data(birds)
species.names <- birds[,2]
specimen.Number <- nrow(birds)
rownames(birds) <- species.names
Nuc.count <- count.function(birds, specimen.Number, 648)
frequency.matrix <- ffrequency.matrix.function(Nuc.count, 648)
birdSpec.freq <- specimen.frequencies(frequency.matrix, birds, specimen.Number, species.names, 648)
Bird_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)
Sliding.Window(Bird_position_VLFcount, 648)
## End(Not run)
[Package VLF version 1.1 Index]