Browse code

updated documentation

Tom Sherman authored on 02/08/2018 18:51:45
Showing7 changed files

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@@ -151,7 +151,7 @@ checkpointInFile=NULL, transposeData=FALSE, BPPARAM=NULL, ...)
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 #' @importFrom methods new
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 #' @examples
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 #' data(SimpSim)
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-#' scCoGAPS(SimpSim.data)
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+#' scCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())
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 scCoGAPS <- function(data, params=new("CogapsParams"), nThreads=1,
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 messages=TRUE, outputFrequency=500, uncertainty=NULL,
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 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,
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@@ -173,7 +173,7 @@ checkpointInFile=NULL, transposeData=FALSE, BPPARAM=NULL, ...)
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 #' @importFrom methods new
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 #' @examples
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 #' data(SimpSim)
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-#' GWCoGAPS(SimpSim.data)
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+#' GWCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())
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 GWCoGAPS <- function(data, params=new("CogapsParams"), nThreads=1,
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 messages=TRUE, outputFrequency=500, uncertainty=NULL,
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 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,
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@@ -51,8 +51,8 @@ NULL
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 #' GIST gene expression uncertainty matrix from Ochs et al. (2009)
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 #' @docType data
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-#' @name GIST.matrix
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-#' @usage GIST.matrix
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+#' @name GIST.uncertainty
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+#' @usage GIST.uncertainty
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 NULL
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 #' CoGAPS result from running on GIST dataset
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@@ -451,7 +451,7 @@ configure:6353: gcc -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.c  >&
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 configure:6353: $? = 0
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 configure:6353: ./conftest
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 configure:6353: $? = 0
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-configure:6363: result: 806ea:5100800:7ffafbff:bfebfbff
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+configure:6363: result: 806ea:6100800:7ffafbff:bfebfbff
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 configure:6390: checking for x86 cpuid 0x00000007 output
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 configure:6420: gcc -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.c  >&5
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 configure:6420: $? = 0
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@@ -757,7 +757,7 @@ ax_cv_cxx_openmp=-fopenmp
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 ax_cv_gcc_x86_avx_xgetbv_0x00000000=1f:0
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 ax_cv_gcc_x86_avx_xgetbv_=unknown
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 ax_cv_gcc_x86_cpuid_0x00000000=16:756e6547:6c65746e:49656e69
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-ax_cv_gcc_x86_cpuid_0x00000001=806ea:5100800:7ffafbff:bfebfbff
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+ax_cv_gcc_x86_cpuid_0x00000001=806ea:6100800:7ffafbff:bfebfbff
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 ax_cv_gcc_x86_cpuid_0x00000007=0:29c6fbf:0:0
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 ax_cv_gcc_x86_cpuid_0x80000000=80000008:0:0:0
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 ax_cv_gcc_x86_cpuid_0x80000001=0:0:121:2c100800
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@@ -5,12 +5,8 @@
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 \alias{GIST.matrix}
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 \title{GIST gene expression data from Ochs et al. (2009)}
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 \usage{
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-GIST.matrix
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-
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 GIST.matrix
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 }
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 \description{
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 GIST gene expression data from Ochs et al. (2009)
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-
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-GIST gene expression uncertainty matrix from Ochs et al. (2009)
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 }
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new file mode 100644
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@@ -0,0 +1,12 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/Package.R
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+\docType{data}
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+\name{GIST.uncertainty}
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+\alias{GIST.uncertainty}
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+\title{GIST gene expression uncertainty matrix from Ochs et al. (2009)}
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+\usage{
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+GIST.uncertainty
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+}
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+\description{
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+GIST gene expression uncertainty matrix from Ochs et al. (2009)
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+}
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@@ -49,5 +49,5 @@ wrapper around genome-wide distributed algorithm for CoGAPS
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 }
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 \examples{
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 data(SimpSim)
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-GWCoGAPS(SimpSim.data)
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+GWCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())
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 }
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@@ -49,5 +49,5 @@ wrapper around single-cell distributed algorithm for CoGAPS
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 }
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 \examples{
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 data(SimpSim)
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-scCoGAPS(SimpSim.data)
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+scCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())
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 }