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relatedness.md

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NAME

calculate_relatedness

USAGE

calculate_relatedness(snpdata, mat.name="GT", family="Location", sweepRegions=NULL, groups=c("Chogen","DongoroBa"))

DESCRIPTION

calculate_relatedness is a function that measures the relatedmess between all pairs of isolates for any given pair of populations.

OPTIONS

snpdata: an object of class SNPdata
mat.name: the name of the genotype table to be used. default="GT"
from: the name of the column, in the metadata table, to be used to represent the sample's population
sweepRegions: a data frame with the genomic coordinates of the regions of the genome to be discarded
groups: a vector of character. If specified, relatedness will be generated between these groups

RETURN

a SNPdata object with an additional fied: relatedness. This is a list that contains the relatesness data frame and its correspondent matrix. The data frame will contain the following columns:

     1.  iid1: sample ID 1 in pair
     2.  iid2: sample ID 2 in pair
     3.  relatedness: the inferred relateness value