VLF.count.pos {VLF}

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)