GCTA_singleValue {modACDC}

GCTA_singleValue

Description

Function to return the heritability of an external phenotype for a single dataset

Usage

GCTA_singleValue(
  fileLoc,
  externalVar,
  gctaPath,
  remlAlg = 0,
  maxRemlIt = 100,
  numCovars = NULL,
  catCovars = NULL
)

Arguments

fileLoc

absolute file path to bed, bim, and fam files, including prefix

externalVar

vector of length n of external variable values with no ID column; must be in the same sample order as bed, bim, fam files

gctaPath

absolute path to GCTA software

remlAlg

algorithm to run REML iterations in GCTA; 0 = average information (AI), 1 = Fisher-scoring, 2 = EM; default is 0 (AI)

maxRemlIt

the maximum number of REML iterations; default is 100

numCovars

n x c_n matrix of numerical covariates to adjust heritability model for; must be in same person order as fam file; default is NULL

catCovars

n x c_c matrix of categorical covariates to adjust heritability model for; must be in same person order as fam file; default is NULL

Details

Genome-wide Complex Trait Analysis (GCTA) is a suite of C++ functions. In order to use the GCTA functions, the user must specify the absolute path to the GCTA software, which can be downloaded from the Yang Lab website here.

Here, we use GCTA's Genomics REstricted Maximum Likelihood (GREML) method to estimate the heritability of an external phenotype.

Value

Row of GREML output containing heritability point estimate of external data and standard error

Author(s)

Katelyn Queen, [e-mail]

References

Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011 Jan 7;88(1):76-82. doi: 10.1016/j.ajhg.2010.11.011. Epub 2010 Dec 17. PMID: 21167468; PMCID: PMC3014363.

See Also

GCTA software - https://yanglab.westlake.edu.cn/software/gcta/

Examples

externalVar <- c()

# run function; input data before running
## Not run: OSCA_singleValue(fileLoc = "pathHere", 
                  externalVar = externalVar,
                  gctaPath = "pathHere")
## End(Not run)