@@ -1,22 +1,22 @@

-Package: gcatest

-Title: Genotype Conditional Association TEST

-Version: 1.1.1

-Date: 2015-10-09

-Author: Wei Hao, Minsun Song, John D. Storey

-Maintainer: Wei Hao <[email protected]>, John D. Storey <[email protected]>

-LazyData: true

-Description: GCAT is an association test for genome wide association studies

-    that controls for population structure under a general class of trait.

-    models. 

-Imports:

-    lfa

-Depends:

-    R (>= 3.2)

-Suggests:

-    knitr,

-    ggplot2

-VignetteBuilder: knitr

-License: GPL-3

-biocViews: SNP, DimensionReduction, PrincipalComponent, GenomeWideAssociation

-BugReports: https://github.com/StoreyLab/gcatest/issues

-URL: https://github.com/StoreyLab/gcatest

+Package: gcatest

+Title: Genotype Conditional Association TEST

+Version: 1.3.2

+Date: 2015-10-09

+Author: Wei Hao, Minsun Song, John D. Storey

+Maintainer: Wei Hao <[email protected]>, John D. Storey <[email protected]>

+LazyData: true

+Description: GCAT is an association test for genome wide association studies

+    that controls for population structure under a general class of trait.

+    models. 

+Imports:

+    lfa

+Depends:

+    R (>= 3.2)

+Suggests:

+    knitr,

+    ggplot2

+VignetteBuilder: knitr

+License: GPL-3

+biocViews: SNP, DimensionReduction, PrincipalComponent, GenomeWideAssociation

+BugReports: https://github.com/StoreyLab/gcatest/issues

+URL: https://github.com/StoreyLab/gcatest

@@ -78,6 +78,10 @@ colnames(dat) = "gcat_p"

 ggplot(dat, aes(gcat_p, ..density..)) + geom_histogram(binwidth=1/20) + theme_bw()

 @

+\section{Data Input}

+

+The \texttt{lfa} package provides the function \texttt{read.bed} for parsing PLINK binary genotypes (extension: \texttt{.bed}) into an R object of the format needed for the \texttt{gcat} function.

+

 \bibliographystyle{plain}

 \bibliography{gcatest}