VLF (version 1.1)

VLF.count.pos: 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)

Value

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

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.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

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

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_specimen_VLFcount <- VLF.count.spec(birdSpec.freq, 0.001, 648)
Bird_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)