fastlmmGWAS
: Factored Spectrally Transformed Linear Mixed Model GWASR 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.
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)
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.
A text file with GWAS statistics. Manhattan plot and QQ-Plot.
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).
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