@@ -1,6 +1,6 @@

 Package: qmtools

 Title: Quantitative Metabolomics Data Processing Tools

-Version: 1.3.0

+Version: 1.3.1

 Authors@R: c(

     person(given = "Jaehyun",

            family = "Joo",

@@ -16,8 +16,10 @@ Description: The qmtools (quantitative metabolomics tools) package provides

              standard SummarizedExperiment class. This includes functions for

              imputation, normalization, feature filtering, feature clustering,

              dimension-reduction, and visualization to help users prepare data

-             for statistical analysis. Several functions in this package could

-             also be used in other types of omics data.

+             for statistical analysis. This package also offers a convenient way

+             to compute empirical Bayes statistics for which metabolic features

+             are different between two sets of study samples. Several functions

+             in this package could also be used in other types of omics data.

 License: GPL-3

 Encoding: UTF-8

 Roxygen: list(markdown = TRUE)

@@ -68,6 +68,7 @@ importFrom(limma,normalizeCyclicLoess)

 importFrom(limma,topTable)

 importFrom(methods,is)

 importFrom(patchwork,plot_layout)

+importFrom(stats,as.formula)

 importFrom(stats,cor)

 importFrom(stats,cutree)

 importFrom(stats,dist)

@@ -83,6 +84,8 @@ importFrom(stats,reshape)

 importFrom(stats,residuals)

 importFrom(stats,sd)

 importMethodsFrom(SummarizedExperiment,"assay<-")

+importMethodsFrom(SummarizedExperiment,"colData<-")

 importMethodsFrom(SummarizedExperiment,"rowData<-")

 importMethodsFrom(SummarizedExperiment,assay)

+importMethodsFrom(SummarizedExperiment,colData)

 importMethodsFrom(SummarizedExperiment,rowData)

@@ -1,6 +1,6 @@

 ##' @importClassesFrom SummarizedExperiment SummarizedExperiment

 ##' @importMethodsFrom SummarizedExperiment assay assay<-

-##' @importMethodsFrom SummarizedExperiment rowData rowData<-

+##' @importMethodsFrom SummarizedExperiment rowData rowData<- colData colData<-

 ##' @importFrom grDevices dev.flush dev.hold

 ##' @importFrom graphics Axis box mtext par points rect strwidth text

 ##' @importFrom methods is

@@ -12,6 +12,7 @@

 ##' @importFrom ggplot2 geom_segment scale_x_continuous scale_y_continuous

 ##' @importFrom ggplot2 sec_axis geom_boxplot geom_violin element_text

 ##' @importFrom patchwork plot_layout

+##' @importFrom stats as.formula

 ##' @importFrom limma normalizeCyclicLoess lmFit eBayes topTable makeContrasts

 ##'   contrasts.fit

@@ -95,9 +95,9 @@ Function to make a comparisons between two groups in study samples with a

 \details{

 This function provides a simplified interface of fitting a linear model to

 make a comparison of interest using the \link[limma:lmFit]{limma::lmFit}, \link[limma:ebayes]{limma::eBayes}, and

-\link[limma:toptable]{limma::topTable} functions. For more flexible model specification (e.g.,

+\link[limma:toptable]{limma::topTable} functions. For more flexible model specifications (e.g.,

 interaction model, multi-level model), please use a standard workflow

-outlined in the \code{limma} package manual.

+outlined in the \code{limma} package user's guide.

 }

 \examples{

@@ -6,7 +6,7 @@

 \alias{qmtools-package}

 \title{qmtools: Quantitative Metabolomics Data Processing Tools}

 \description{

-The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. Several functions in this package could also be used in other types of omics data.

+The qmtools (quantitative metabolomics tools) package provides basic tools for processing quantitative metabolomics data with the standard SummarizedExperiment class. This includes functions for imputation, normalization, feature filtering, feature clustering, dimension-reduction, and visualization to help users prepare data for statistical analysis. This package also offers a convenient way to compute empirical Bayes statistics for which metabolic features are different between two sets of study samples. Several functions in this package could also be used in other types of omics data.

 }

 \details{

 The qmtools package provides six categories of important functions: