dartR: gl.report.hamming – R documentation

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gl.report.hamming

Calculates the pairwise Hamming distance between DArT trimmed DNA sequences

Description

Hamming distance is calculated as the number of base differences between two sequences which can be expressed as a count or a proportion. Typically, it is calculated between two sequences of equal length. In the context of DArT trimmed sequences, which differ in length but which are anchored to the left by the restriction enzyme recognition sequence, it is sensible to compare the two trimmed sequences starting from immediately after the common recognition sequence and terminating at the last base of the shorter sequence.

Usage

gl.report.hamming(
  x,
  rs = 5,
  boxplot = "adjusted",
  range = 1.5,
  threshold = 3,
  taglength = 69,
  probar = FALSE,
  verbose = 2
)

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`rs`	– number of bases in the restriction enzyme recognition sequence [default 5]
`boxplot`	– if 'standard', plots a standard box and whisker plot; if 'adjusted', plots a boxplot adjusted for skewed distributions [default 'adjusted']
`range`	– specifies the range for delimiting outliers [default = 1.5 interquartile ranges]
`threshold`	minimum acceptable base pair difference for display on the whisker plot and histogram [default 3 bp]
`taglength`	– typical length of the sequence tags [default 69]
`probar`	– if TRUE, then a progress bar is desplayed on long loops [default TRUE]
`verbose`	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Details

Hamming distance can be computed by exploiting the fact that the dot product of two binary vectors x and (1-y) counts the corresponding elements that are different between x and y. This approach can also be used for vectors that contain more than two possible values at each position (e.g. A, C, T or G).

If a pair of DNA sequences are of differing length, the longer is truncated.

The algorithm is that of Johann de Jong https://johanndejong.wordpress.com/2015/10/02/faster-hamming-distance-in-r-2/ as implimented in utils.hamming.r

A histogram and whiskerplot can be requested. Both display a user specified value for the minumum acceptable Hamming distance.

Value

Tabulation of loc that will be lost on filtering, against values of the threshold

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

out <- gl.report.hamming(testset.gl)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29