diff options
Diffstat (limited to 'doc/manual.tex')
| -rw-r--r-- | doc/manual.tex | 21 |
1 files changed, 7 insertions, 14 deletions
diff --git a/doc/manual.tex b/doc/manual.tex index 555d766..dc0aadf 100644 --- a/doc/manual.tex +++ b/doc/manual.tex @@ -75,7 +75,7 @@ association studies (GWAS). It fits a univariate linear mixed model (LMM) for marker association tests with a single phenotype to account for population stratification and sample structure, and for estimating the proportion of variance in phenotypes explained (PVE) by typed -genotypes (i.e. "chip heritability") \cite{Zhou:2012}. It fits a +genotypes (i.e. ``chip heritability'' or ``SNP heritability'') \cite{Zhou:2012}. It fits a multivariate linear mixed model (mvLMM) for testing marker associations with multiple phenotypes simultaneously while controlling for population stratification, and for estimating genetic correlations @@ -139,8 +139,8 @@ score). GEMMA obtains either the maximum likelihood estimate (MLE) or the restricted maximum likelihood estimate (REML) of $\lambda$ and $\beta$, and outputs the corresponding $p$ value. -In addition, GEMMA estimates the PVE by typed genotypes or ``chip -heritability". +In addition, GEMMA estimates the PVE by typed genotypes or ``chip or +SNP heritability''. \subsubsection{Multivariate Linear Mixed Model} GEMMA can fit a multivariate linear mixed model in the following form: @@ -307,19 +307,12 @@ platform. The binary executable of GEMMA works well for a reasonably large number of individuals (say, for example, the ``-eigen " option works -for at least 45,000 individuals). Due to the outdated computation -environment the software was compiled on, however, for larger sample -size and for improved computation efficiency, it is recommended to -compile GEMMA on user's own modern computer system. +for at least 45,000 individuals). If you want to compile GEMMA by yourself, you will need to download the source code, and you will need a standard C/C++ compiler such as -GNU gcc, as well as the GSL and LAPACK libraries. You will need to -change the library paths in the Makefile accordingly. A sample -Makefile is provided along with the source code. For details on -installing GSL library, please refer to -\url{http://www.gnu.org/s/gsl/}. For details on installing LAPACK -library, please refer to \url{http://www.netlib.org/lapack/}. +GNU gcc, as well as GSL and OpenBLAS libraries. A sample +Makefile is provided along with the source code. \newpage @@ -334,7 +327,7 @@ genotypes and using BIMBAM files for phenotypes) will result in unwanted errors. BIMBAM format is particularly useful for imputed genotypes, as PLINK codes genotypes using 0/1/2, while BIMBAM can accommodate any real values between 0 and 2 (and any real values if -paired with ``-notsnp" option). In addition, to estimate variance +paired with ``-notsnp'' option). In addition, to estimate variance components using summary statistics, GEMMA requires two other input files: one contains marginal z-scores and the other contains SNP category. |