Description Usage Arguments Details Value Author(s) See Also Examples

This function returns a pairwise similarity matrix based on how many loci or the proportion of loci shared between individuals.

1 | ```
locus.dist(pyIn, proportional = TRUE, upper = TRUE, diagonal = TRUE)
``` |

`pyIn` |
an object of class |

`proportional` |
set to |

`upper` |
set to |

`diagonal` |
set to |

Under the `proportional = TRUE`

option, this function normalizes based on all loci
in the dataset. Thus, two individuals that share 100
have sequences for only 90
0.9 instead of 1.0.

A square matrix with individuals as the rows and columns, and proportions or whole numbers in the cells

Andrew Hipp

1 2 3 4 5 6 | ```
data(oak.rads)
temp <- locus.dist(oak.rads, proportional = TRUE)
diag(temp) # this is how well everyone sequenced as a proportion
temp <- locus.dist(oak.rads, proportional = FALSE)
temp[c(1,28),]# how well did a successful sequencing do in comparison to a poor sequencing?
temp[6:7,] # ... and 2010 sequencing (upper row) vs. 2012 sequencing of the same library?
``` |

RADami documentation built on May 30, 2017, 8:23 a.m.

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