computeGRM

path to PLINK binary .bed/.bim/.fam files

bedfullheader

grmfullheader

gctaname

path to a file listing the subset of individuals to include in GRM calculation (2 columns labeled: FID, IID)

idfile

path to a file listing a subset of SNPs, one per line and no column header, to included in the GRM calculation, default is to include all autosomal SNPs in the .bim file

snpfile

This function calls the software GCTA to calculate the genetic relationship matrix from all autosomal SNP genotype data in PLINK binary PED file format.

This package provides functions to generate correlation
        matrices from SNP, gene expression, methylation or other
        'omics' datasets and to use these matrices to predict the
        phenotype of an individual by using the phenotypes of the
        remaining individuals through kriging. Kriging is a
        geostatistical method for optimal prediction or best unbiased
        linear prediction. It consists of predicting the value of a
        variable at an unobserved location as a weighted sum of the
        variable at observed locations. Intuitively, it works as a
        reverse linear regression: instead of computing correlation
        (univariate regression coefficients are simply scaled
        correlation) between a dependent variable Y and independent
        variables X, it uses known correlation between X and Y to
        predict Y.

computeGRM: Compute the genetic relatedness matrix

Description

Usage

Arguments

Value

References