VLF (version 1.1)

Sliding.Window: Sliding Window

Description

Creates a sliding window analysis plot for the VLFs in a matrix of sequences.

Usage

Sliding.Window(VLF, seqlength, n = 30)

Value

A sliding window plot for the VLFs in each position of the barcode averaged over n.

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).

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument VLF can be calculated using the function VLF.count.pos for all VLFs, or find.singles for singleton and shared VLFs.

Examples

if (FALSE) 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)