Sliding.Window: Sliding Window

In VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

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)

VLF documentation built on April 12, 2025, 1:22 a.m.