Release 1.0 - updated according to the feedback from CRAN

DESCRIPTION

@@ -1,8 +1,9 @@
 Package: DESnowball
 Type: Package
-Title: Bagging with Distance-based Regression for Differential Gene Expression Analyses 
+Title: Bagging with Distance-based Regression for Differential Gene Expression
+    Analyses
 Version: 1.0
-Date: 2013-07-20
+Date: 2014-1-2
 Author: Yaomin Xu <[email protected]>
 Maintainer: Yaomin Xu <[email protected]>
 Depends:
@@ -13,6 +14,10 @@ Imports:
     MASS,
     parallel,
     cluster
-Description: This package implements a statistical data mining method to compare whole genome gene expression
-    profiles with respect to the presence of a recurrent genetic disturbance event to identify the affected target genes.
+Description: This package implements a statistical data mining method to
+    compare whole genome gene expression profiles, with respect to the presence
+    of a recurrent genetic disturbance event, to identify the affected target
+    genes.
 License: GPL-3
+URL: https://github.com/snowball-project/DESnowball
+BugReports: https://github.com/snowball-project/DESnowball/issues

R/sb-expression-data.r

@@ -1,8 +1,6 @@
 #' Gene expression data of 14 patients
-
-#' A demo dataset containing 6597 gene expression profiles on 14 patients, the corresponding
-#' mutation status is provided in \code{\link{sb.mutation}}
-
+#'
+#' A demo dataset containing 6597 gene expression profiles on 14 patients, the corresponding mutation status is provided in \code{\link{sb.mutation}}
 #' @docType data
 #' @keywords datasets
 #' @format A data.frame with 6597 rows and 14 variables

R/sb-mutation-data.r

@@ -1,7 +1,6 @@
 #' Mutation status of 14 patients
-
+#'
 #' A character vector indicating the mutation status of 14 patients
-
 #' @docType data
 #' @keywords datasets
 #' @format A character vector of 14 elements

README.md

@@ -3,11 +3,11 @@
 ## About
 The DESnowball package implements a statistical data mining method that compares the whole genome gene 
 expression profiles with respect to the presence of a recurrent genetic disturbance event (
-e.g. a recurrent driver mutation) to identify the target genes affected by the event.
+e.g. a recurrent driver mutation) to identify the affected target genes.
 
-The input data for the snowball analysis are the profiling of the whole genome gene expression profiles 
+The input data for the snowball analysis are the whole genome gene expression profiles 
 and the mutation status of a recurrent genetic event on a group of samples. The analysis has 
-been tested on the TCGA primary tumor samples. The minimum sample size required per group is three. 
+been tested on the TCGA melanoma primary tumor samples. The minimum sample size required per group is three. 
 
 ## Installation
 From R:
@@ -32,3 +32,12 @@ Example: snowball analysis on the demo dataset included in the package
     plotJn(sb, sb.sel)
     # get the significant gene list
     top.genes <- toplist(sb.sel)
+## References
+Xu, Y. and Sun, J. (2005) PfCluster: a new cluster analysis procedure for gene expression profiles. Presented at a conference on Nonparametric Inference and Probability With Applications to Science honoring Michael Woodroofe; September 24-25, 2005; Ann Arbor, Mich, 2005. 
+
+McArdlei, B.H. and Anderson, M.J. (2001) Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82(1): 290-297.
+
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling combined with distance-based regression to discover transcriptional consequences of driver mutation, manuscript.
+
+Guo, X., Xu, Y. and Zhao, Z.. Driver mutation BRAF regulates cell proliferation and apoptosis via MITF in the pathogenesis of melanoma, manuscript.
+

man/DESnowball-package.Rd

@@ -4,22 +4,23 @@
 \title{A R package implemented Snowball approach (see references)}
 \description{
 Genome-wide differential gene expression analysis with
-respect to the presence of a recurrent driver mutation
+respect to the presence of a recurrent genetic disturbance
+(a driver mutation)
 }
 \details{
-The DESnowball package implements the Snowball approach
-(see references). It is a differential gene expression
-analysis tool that compares the whole genome gene
-expression profiles measured on tumor samples with vs.
-without a recurrent driver mutation.
+The DESnowball package implements a differential gene
+expression analysis tool that compares the whole genome
+gene expression profiles on samples relative to the
+presence of a recurrent genetic disturbance (driver
+mutation).
 
 The input data for the snowball analysis are the profiling
 of the whole genome gene expression and the mutation status
-of a recurrent driver mutation on a group of patient
-samples. The analysis has been tested on the primary tumor
-samples and the minimum sample size required per group is
-three. Snowball does not require a balanced design between
-groups (see references).
+of a recurrent genetic event on a group of samples. The
+analysis has been tested on human primary tumor samples and
+the minimum sample size required per group is three.
+Snowball does not require a balanced design between groups
+(see references).
 
 The main function of the package is \code{\link{snowball}},
 it requires two input data, named \code{y} and \code{X},
@@ -45,13 +46,23 @@ and \code{\link{toplist}} to report the top genes based on
 the user provided cutoff.
 }
 \references{
-Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao.
-Snowball: resampling combined with distance-based
-regression to discover transcriptional consequences of
-driver mutation (submitted)
+Xu, Y. and Sun, J. (2005) PfCluster: a new cluster analysis
+procedure for gene expression profiles. Presented at a
+conference on Nonparametric Inference and Probability With
+Applications to Science honoring Michael Woodroofe;
+September 24-25, 2005; Ann Arbor, Mich, 2005.
 
-Xingyi Guo, Yaomin Xu, Zhongming Zhao. Driver mutation BRAF
+McArdlei, B.H. and Anderson, M.J. (2001) Fitting
+multivariate models to community data: A comment on
+distance-based redundancy analysis. Ecology 82(1): 290-297.
+
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
+
+Guo, X., Xu, Y. and Zhao, Z.. Driver mutation BRAF
 regulates cell proliferation and apoptosis via MITF in the
-pathogenesis of melanoma (submitted)
+pathogenesis of melanoma, manuscript.
 }
 

man/sb.expression.Rd

@@ -1,15 +1,22 @@
 \docType{data}
 \name{sb.expression}
 \alias{sb.expression}
-\title{Gene expression data of 14 patients
-A demo dataset containing 6597 gene expression profiles on 14 patients, the corresponding
-mutation status is provided in \code{\link{sb.mutation}}}
+\title{Gene expression data of 14 patients}
 \format{A data.frame with 6597 rows and 14 variables}
 \description{
-Gene expression data of 14 patients A demo dataset
-containing 6597 gene expression profiles on 14 patients,
-the corresponding mutation status is provided in
-\code{\link{sb.mutation}}
+A demo dataset containing 6597 gene expression profiles on
+14 patients, the corresponding mutation status is provided
+in \code{\link{sb.mutation}}
+}
+\references{
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
+
+Guo, X., Xu, Y. and Zhao, Z.. Driver mutation BRAF
+regulates cell proliferation and apoptosis via MITF in the
+pathogenesis of melanoma, manuscript.
 }
 \keyword{datasets}
 

man/sb.mutation.Rd

@@ -1,12 +1,21 @@
 \docType{data}
 \name{sb.mutation}
 \alias{sb.mutation}
-\title{Mutation status of 14 patients
-A character vector indicating the mutation status of 14 patients}
+\title{Mutation status of 14 patients}
 \format{A character vector of 14 elements}
 \description{
-Mutation status of 14 patients A character vector
-indicating the mutation status of 14 patients
+A character vector indicating the mutation status of 14
+patients
+}
+\references{
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
+
+Guo, X., Xu, Y. and Zhao, Z.. Driver mutation BRAF
+regulates cell proliferation and apoptosis via MITF in the
+pathogenesis of melanoma, manuscript.
 }
 \keyword{datasets}
 

man/select.features.Rd

@@ -31,4 +31,10 @@ Gene selection based on the statistical significances
 according to the Snowball approach (see references for more
 details).
 }
+\references{
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
+}
 

man/snowball.Rd

@@ -148,9 +148,9 @@ top.genes <- toplist(sb.sel)
 }
 }
 \references{
-Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao.
-Snowball: Resampling combined with distance-based
-regression to discover transcriptional consequences of
-driver mutation (submitted)
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
 }
 

man/toplist.Rd

@@ -16,9 +16,9 @@ a data.frame with two columns \code{RD} and \code{pvalue}
 Report the top list based on p values.
 }
 \references{
-Yaomin Xu, Xingyi Guo, Jiayang Sun, Zhongming Zhao.
-Snowball: Resampling combined with distance-based
-regression to discover transcriptional consequences of
-driver mutation (submitted)
+Xu, Y., Guo, X., Sun, J. and Zhao. Z. Snowball: resampling
+combined with distance-based regression to discover
+transcriptional consequences of driver mutation,
+manuscript.
 }