R: Fraction of k-mers observed at least r times

kmer.frac.curve {preseqR} | R Documentation

## Fraction of k-mers observed at least r times

### Description

`kmer.frac.curve` predicts the expected fraction of k-mers observed at least r times in a high-throughput sequencing experiment given the amount of sequencing

### Usage

      kmer.frac.curve(n, k, read.len, seq, r=2, mt=20)

### Arguments

`n` | A two-column matrix. The first column is the frequency j = 1,2,…; and the second column is N_j, the number of k-mers observed exactly j times in the initial experiment. The first column must be sorted in an ascending order.
`k` | The number of nucleotides in a k-mer.
`read.len` | The average length of a read.
`seq` | The amount of nucleotides sequenced..
`r` | A positive integer. Default is 1.
`mt` | An positive integer constraining possible rational function approximations. Default is 20.

### Details

`kmer.frac.curve` is mainly designed for metagenomics to evaluate how saturated a metagenomic data is.

`kmer.frac.curve` is the fast version of `kmer.frac.curve.bootstrap`. The function does not provide the confidence interval. To obtain the confidence interval along with the estimates, one should use the function `kmer.frac.curve.bootstrap`.

### Value

A two-column matrix. The first column is the amount of sequencing in an experiment. The second column is the estimate of the fraction of k-mers observed at least r times in the experiment.

### Author(s)

Chao Deng

### References

Deng, C and Smith, AD (2016). Estimating the number of species to attain sufficient representation in a random sample. arXiv preprint arXiv:1607.02804

### Examples

    ## load library
    library(preseqR)

    ## import data
    data(SRR061157_k31)

    ## the fraction of 31-mers represented at least 10 times in an experiment when
    ## sequencing 1M, 10M, 100M, 1G, 10G, 100G, 1T nucleotides
    kmer.frac.curve(n=SRR061157_k31, k=31, read.len=100, seq=10^(6:12), r=10, mt=20)

[Package preseqR version 4.0.0 Index]