diff --git a/DESCRIPTION b/DESCRIPTION index fe95c84..bed35f0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,9 +10,9 @@ Maintainer: Yue Fan Description: MQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern. Encoding: UTF-8 License: GPL (>= 2) -Depends: R (>= 3.6.0) +Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.19),foreach,doParallel,parallel,Matrix LinkingTo: Rcpp, RcppArmadillo RoxygenNote: 6.1.1 NeedsCompilation: yes -Packaged: 2019-07-08 20:14:35 UTC; yuef +Packaged: 2019-07-09 12:48:28 UTC; yuef diff --git a/R/IMAGE.R b/R/IMAGE.R index 8875fd1..3eebca0 100644 --- a/R/IMAGE.R +++ b/R/IMAGE.R @@ -35,7 +35,10 @@ #' @author Yue Fan, Shiquan Sun, Xiang Zhou #' @examples #' data(exampledata) -#' res=image(exampledata$geno,exampledata$data,exampledata$K) +#' attach(exampledata) +#' res=image(geno,data,K) +#' closeAllConnections() +#' detach(exampledata) diff --git a/R/exampledata.R b/R/exampledata.R index e2994d3..f51cc94 100644 --- a/R/exampledata.R +++ b/R/exampledata.R @@ -3,6 +3,10 @@ #' A simulated example dataset of IMAGE. #' The variables are as follows: #' +#' @docType data +#' @keywords datasets +#' @name exampledata +#' @usage data(exampledata) #' @format Contains the following objects: #' \describe{ #' \item{geno}{a data list containing 2 haplotypes.} @@ -11,5 +15,8 @@ #' } #' @examples #' data(exampledata) -#' res=image(exampledata$geno,exampledata$data,exampledata$K) +#' attach(exampledata) +#' res=image(geno,data,K) +#' closeAllConnections() +#' detach(exampledata) "exampledata" \ No newline at end of file diff --git a/build/partial.rdb b/build/partial.rdb index dec1d96..bf4ab46 100644 Binary files a/build/partial.rdb and b/build/partial.rdb differ diff --git a/man/exampledata.Rd b/man/exampledata.Rd index 2cecbcc..ee75108 100644 --- a/man/exampledata.Rd +++ b/man/exampledata.Rd @@ -11,7 +11,7 @@ \item{K}{a genetic relationship matrix.} }} \usage{ -exampledata +data(exampledata) } \description{ A simulated example dataset of IMAGE. @@ -19,6 +19,9 @@ The variables are as follows: } \examples{ data(exampledata) -res=image(exampledata$geno,exampledata$data,exampledata$K) +attach(exampledata) +res=image(geno,data,K) +closeAllConnections() +detach(exampledata) } \keyword{datasets} diff --git a/man/image.Rd b/man/image.Rd index 92bffdc..ec9adcf 100644 --- a/man/image.Rd +++ b/man/image.Rd @@ -50,7 +50,10 @@ Binomial mixed models (BMM) are fitted using the penalized quasi-likelihood (PQL } \examples{ data(exampledata) -res=image(exampledata$geno,exampledata$data,exampledata$K) +attach(exampledata) +res=image(geno,data,K) +closeAllConnections() +detach(exampledata) } \references{ Breslow, N.E. and Clayton, D.G. (1993) Approximate Inference in Generalized Linear Mixed Models. Journal of the American Statistical Association 88, 9-25. diff --git a/src/IMAGE.dll b/src/IMAGE.dll new file mode 100644 index 0000000..230bc84 Binary files /dev/null and b/src/IMAGE.dll differ diff --git a/src/IMAGE.o b/src/IMAGE.o new file mode 100644 index 0000000..263f999 Binary files /dev/null and b/src/IMAGE.o differ diff --git a/src/RcppExports.o b/src/RcppExports.o new file mode 100644 index 0000000..1d5d77a Binary files /dev/null and b/src/RcppExports.o differ diff --git a/src/rcpparma_hello_world.o b/src/rcpparma_hello_world.o new file mode 100644 index 0000000..600a027 Binary files /dev/null and b/src/rcpparma_hello_world.o differ