VLF.count.pos: VLF Count for Sequence Positions

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

VLF Count for Sequence Positions

Description

Calculates the number of very low frequency variants (VLFs) in each position in a matrix of sequences.

Usage

VLF.count.pos(freq, p, seqlength)

Arguments

freq	A matrix of frequencies for each specimen.
p	A very low frequency variant designation cut off frequency. Any frequency in the freq matrix below this value is considered to be a very low frequency variant.
seqlength	The length of the sequences.

Details

The argument freq can be calculated using the specimen.frequencies function.

Value

A vector containing the number of VLFs for each position in the sequence.

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_specimen_VLFcount <- VLF.count.spec(birdSpec.freq, 0.001, 648)
Bird_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)
## End(Not run)

VLF documentation built on Aug. 18, 2022, 5:06 p.m.