fastlmmGWAS: Factored Spectrally Transformed Linear Mixed Model GWAS

Description

R interface to perform GWAS using Factored Spectrally Transformed Linear Mixed Models (FaST-LMM). FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models is a program for performing single-SNP and SNP-set genome-wide association studies (GWAS) on extremely large data sets. It runs on both Windows and Linux systems, and has been tested on data sets with over 120,000 individuals.

Usage

fastlmmGWAS(formula = NULL, geno, phen, IDname, map, nPC = 0,
  useG = FALSE, MAF = 0.01, HWE = 1e-10, HZ = 0.01, SNPcall = 0.9,
  INDcall = 0.9, rmMAF = TRUE, rmHWE = TRUE, rmHZ = TRUE,
  rmSNPCall = TRUE, rmINDCall = FALSE, rSrcDir = NULL, phenName = NULL,
  MarkerRow = TRUE)

Arguments

Argument	Description
formula	A formula specifying the model.
geno	It is the name of markers file.
phen	It is the name of phenotypes file.
IDname	It is the individual's name.
map	It is the map file with colukns in the following order: Marker, Chromosome and Position.
nPC	Number of principal components if any.
useG	A logical value indicating whether the kinship must be used.
MAF	A value indicating the Minor Allele Frequency.
HWE	A value indicating the Hardy-Weinberg Equilibrium.
HZ	A value indicating the SNP heterozygosity.
SNPcall	A value indicating the SNP call rate.
INDcall	A value indicating the individual call rate for autosomal SNPs.
rmMAF	A logical value indicating whether markers sould be removed based on MAF.
rmHWE	A logical value indicating whether markers sould be removed based on HWE.
rmHZ	A logical value indicating whether markers sould be removed based on HZ.
rmSNPCall	A logical value indicating markers sould be removed based on SNP call rate.
rmINDCall	A logical value indicating markers sould be removed based on individual call rate.
rSrcDir	Optional path to the folder where the FaST-LMM programm are.
MarkerRow	A logical value indicating whether the markers are in rows.

Value

A text file with GWAS statistics. Manhattan plot and QQ-Plot.

References

C. Lippert, J. Listgarten, Y. Liu, C.M. Kadie, R.I. Davidson, and D. Heckerman. FaST Linear Mixed Models for Genome-Wide Association Studies. Nature Methods 8: 833-835, Oct 2011 (doi:10.1038/nmeth.1681).

C. Widmer, C. Lippert, O. Weissbrod, N. Fusi, C.M. Kadie, R.I. Davidson, J. Listgarten, and D. Heckerman. Further Improvements to Linear Mixed Models for Genome-Wide Association Studies. Scientific Reports 4, 6874, Nov 2014 (doi:10.1038/srep06874).