calculate_relatedness: Estimate the relatedness between pairs of isolates

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

Estimate the relatedness between pairs of isolates

Description

Estimate the relatedness between pairs of isolates

Usage

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

Arguments

snpdata	SNPdata object
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. This should contain the following 3 columns: Chrom: the chromosome ID Start: the start position of the region on the chromosome End: the end position of the region on the chromosome
groups	a vector of character. If specified, relatedness will be generated between these groups

Details

The relatedness calculation is based on the model developed by Aimee R. Taylor and co-authors. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009101

Value

SNPdata object with an extra field: relatedness. This will contain the relatedness data frame of 3 columns and its correspondent matrix

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.