Skip to contents

Nucleotide diversity

Source: R/pi.R
pi.Rd

Calculates the nucleotide diversity (Nei & Li, 1979).

To get an estimate with the consensus reads, use the function summary_haplotypes found in the package stackr. The estimate in summary_haplotypes integrates the consensus markers found in STACKS populations.haplotypes.tsv file. Both radr and stackr functions requires stringdist package.

The read.length argument below is used directly in the calculations. To be correctly estimated, the reads obviously need to be of identical size...

Usage

pi(
  data,
  read.length = NULL,
  parallel.core = parallel::detectCores() - 1,
  path.folder = NULL,
  verbose = TRUE
)

Arguments

data

(4 options) A file or object generated by radr:

  • tidy data

  • Genomic Data Structure (GDS)

How to get GDS and tidy data ? Use read_genome to import supported formats and tidy_genome when a tidy table is needed.

read.length

(integer, optional) The length in nucleotide of your reads. By default it is estimated from the data using the column COL. Default: read.length = NULL.

parallel.core

Number of workers available for parallel operations. Default: parallel.core = parallel::detectCores() - 1.

path.folder

(path, optional) By default will print results in the working directory. Default: path.folder = NULL.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = TRUE.

Value

The function returns a list with the function call and:

  1. $pi.individuals: the pi estimated for each individual

  2. $pi.populations: the pi statistics estimated per populations and overall.

  3. $boxplot.pi: showing the boxplot of Pi for each populations and overall.

use $ to access each #' objects in the list.

Note

Thanks to Anne-Laure Ferchaud for very useful comments on previous version of this function.

References

Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76, 5269–5273.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
require(stringdist)
# The simplest way to run the function:
pi.sum <- radr::pi(data = "brook.charr.gds")
} # }