callRelatedness {BREADR} | R Documentation |

## callRelatedness

### Description

A function that takes PMR observations, and (given a prior distribution for degrees of relatedness) returns the posterior probabilities of all pairs of individuals being (a) the same individual/twins, (b) first-degree related, (c) second-degree related or (d) "unrelated" (third-degree or higher). The highest posterior probability degree of relatedness is also returned as a hard classification. Options include setting the background relatedness (or using the sample median), a minimum number of overlapping SNPs if one uses the sample median for background relatedness, and a minimum number of overlapping SNPs for including pairs in the analysis.

### Usage

```
callRelatedness(
pmr_tibble,
class_prior = rep(0.25, 4),
average_relatedness = NULL,
median_co = 500,
filter_n = 1
)
```

### Arguments

`pmr_tibble` |
a tibble that is the output of the processEigenstrat function. |

`class_prior` |
the prior probabilities for same/twin, 1st-degree, 2nd-degree, unrelated, respectively. |

`average_relatedness` |
a single numeric value, or a vector of numeric values, to use as the average background relatedness. If NULL, the sample median is used. |

`median_co` |
if average_relatedness is left NULL, then the minimum cutoff for the number of overlapping snps to be included in the median calculation is 500. |

`filter_n` |
the minimum number of overlapping SNPs for which pairs are removed from the entire analysis. If NULL, default is 1. |

### Value

results_tibble: A tibble containing 13 columns:

row: The row number

pair: the pair of individuals that are compared.

relationship: the highest posterior probability estimate of the degree of relatedness.

pmr: the pairwise mismatch rate (mismatch/nsnps).

sd: the estimated standard deviation of the pmr.

mismatch: the number of sites which did not match for each pair.

nsnps: the number of overlapping snps that were compared for each pair.

ave_re;: the value for the background relatedness used for normalisation.

Same_Twins: the posterior probability associated with a same individual/twins classification.

First_Degree: the posterior probability associated with a first-degree classification.

Second_Degree: the posterior probability associated with a second-degree classification.

Unrelated: the posterior probability associated with an unrelated classification.

BF: A strength of confidence in the Bayes Factor associated with the highest posterior probability classification compared to the 2nd highest. (No longer included)

### Examples

```
callRelatedness(counts_example,
class_prior=rep(0.25,4),
average_relatedness=NULL,
median_co=5e2,filter_n=1
)
```

*BREADR*version 1.0.1 Index]