README.md

In camult/easyGWAS: easyGWAS

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).

camult/easyGWAS documentation built on May 6, 2019, 3:30 p.m.