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

View source: R/population_stats.R

Given a set of allele frequencies, this function estimates the Polymorphic Information Content (PIC) for each locus, within and/or across populations.

1 2 3 |

`freqs` |
A data frame of allele frequencies, such as those output by |

`pops` |
An optional characer vector containing names of populations to include. |

`loci` |
An optional character vector containing names of loci to include. |

`bypop` |
If |

`overall` |
If |

PIC is estimated as:

*
1 - (∑ {i = 1} to {n} p_i^2) - ∑ {i = 1} to {n - 1} ∑ {j = i + 1} to {n} 2 * p_i^2 * p_j^2*

according to Botstein et al. (1980), where *p_i* and *p_j* are allele frequencies at alleles
*i* and *j*, respectively, and *n* is the number of alleles.

The higher this value is, the more useful a marker is for distinguishing individuals and understanding relationships among them.

A matrix, with loci in columns, and populations and/or “Overall” in rows. Each element of the matrix contains a PIC value.

Lindsay V. Clark

Botstein, M., White, R. L., Skolnick, M. and Davis, R. W. (1980) Construction of
a genetic linkage map in man using restriction fragment length polymorphisms.
*American Journal of Human Genetics* **32**, 314–331.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
# generate allele frequencies for this example
myfreq <- data.frame(row.names = c("pop1", "pop2"),
Genomes = c(20,30),
loc1.124 = c(0.1, 0.25),
loc1.126 = c(0.2, 0),
loc1.128 = c(0.05, 0.4),
loc1.130 = c(0.3, 0.1),
loc1.132 = c(0.1, 0.1),
loc1.134 = c(0.25, 0.15),
loc2.150 = c(0.4, 0.5),
loc2.155 = c(0.3, 0.2),
loc2.160 = c(0.3, 0.3))
# estimate PIC
PIC(myfreq)
``` |

polysat documentation built on June 8, 2018, 1:04 a.m.

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