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NAME

calculate_LD

USAGE

calculate_LD(snpdata, min.r2=0.2, inter.chrom=FALSE, chroms=NULL)

DESCRIPTION

calculate_LD is a function that is used to calculate LD R^2 between pairs of loci using the vcftools program.

OPTIONS

snpdata: an object of class SNPdata
min.r2: the minimum R^2 value below which the LD value is not reported
inter.chrom: whether to calculate inter-chromosomal LD
chroms: a vector of chromosome names for which LD should be calculated

RETURN

a SNPdata object with an additional field: LD. this is a data frame with 6 columns:

     1.  CHR1: the chromosome of the first SNP
     2.  POS1: the position of the first SNP in the chromosome
     3.  CHR2: the chromosome of the second SNP
     4.  POS2: the position of the second SNP in the chromosome
     5.  N_INDV: the number of samples used to calculate the R^2
     6.  R^2: the resulting R^2 values