get_corr_chr: Calculate Correlation in Local Ancestry (K = 3)

In GrindeLab/STEAMcpp_mirror:

Description

Calculate the correlation of local ancestry vectors for a single chromosome. Code is currently only applicable to admixed populations with three ancestral populations.

Usage

get_corr_chr(
  chrom,
  binsize = 0.5,
  map,
  pop1.gds,
  pop2.gds,
  pop3.gds,
  verbose = TRUE
)

Arguments

chrom	chromosome number that you are analyzing
binsize	size (in cM) of distance bins for calculating correlation; default = 0.5 cM
map	map file; data frame with, at minimum, columns 'chr' and 'cM'
pop1.gds	name of GDS file storing local ancestry calls for chrom of interest, with alleles coded as 1 = pop 1 ancestry, 0 = pop 2 or 3
pop2.gds	name of GDS file storing local ancestry calls for chrom of interest, with alleles coded as 1 = pop 2 ancestry, 0 = pop 1 or 3
pop3.gds	name of GDS file storing local ancestry calls for chrom of interest, with alleles coded as 1 = pop 3 ancestry, 0 = pop 1 or 2
verbose	do you want to print updates to screen; default = TRUE

Value

A data table with the observed correlation in local ancestry vectors for a subset of loci on this chromosome.

See Also

get_g and combine_corr_chr

GrindeLab/STEAMcpp_mirror documentation built on Dec. 31, 2020, 12:05 p.m.