@@ -111,7 +111,6 @@ exportMethods(poplin_data_names)

 exportMethods(poplin_reduced)

 exportMethods(poplin_reduced_list)

 exportMethods(poplin_reduced_names)

-exportMethods(rbind)

 exportMethods(show)

 import(methods)

 importClassesFrom(S4Vectors,DataFrame)

@@ -1,10 +1,63 @@

+##' Combining or subsetting poplin objects

+##'

+##' Methods to combine multiple \linkS4class{poplin} objects by row or column,

+##' or to subset a \linkS4class{poplin} object by row or column.

+##'

+##' @section Combining:

+##'

+##' In the code snippets below, \code{...} represents multiple

+##' \linkS4class{poplin} objects to be combined.

+##'

+##' \describe{

+##' \item{\code{rbind(..., deparse.level = 1)}:}{

+##'

+##' Take a sequence of poplin objects in \code{...} and combine by rows. Note

+##' that all objects in ... must have the exact same values for

+##' [poplin_data_list]. See \code{?}[rbind] for the interpretation of

+##' \code{deparse.level}.

+##'

+##' }

+##' \item{\code{cbind(..., deparse.level = 1)}:}{

+##'

+##' Take a sequence of poplin objects in \code{...} and combine by columns. Note

+##' that all objects in ... must have the same values of [poplin_reduced_names].

+##' Dimension reduction results with the same name across the objects will be

+##' combined row-wise to create the corresponding entry in the output object.

+##' See \code{?}[cbind] for the interpretation of \code{deparse.level}.

+##'

+##' }

+##' }

+##'

+##' Refer to \code{help("SummarizedExperiment-class", package =

+##' "SummarizedExperiment")} for details on how \code{rowData}, \code{colData},

+##' and \code{metadata} are combined in the output object.

+##'

+##' @section Subsetting:

+##'

+##' In the code snippets below, \code{x} is a \linkS4class{poplin}

+##' object.

+##'

+##' \describe{

+##'

+##' \item{\code{x[i, j]}, \code{x[i, j] <- value}:}{\code{i} and \code{j} are

+##' indices specifying the rows and columns to extract or replace. Indices can

+##' be a logical, integer, character vector, or empty (missing). \code{value}

+##' must be a poplin object with the dimension and assay elements consistent

+##' with the subset \code{x[i, j]} being replaced. \code{value} is also expected

+##' to have the same name and order of [poplin_data_names] (and

+##' [poplin_reduced_names] as well if \code{j} is specified) as \code{x}.}

+##'

+##' }

+##'

+##' @importFrom BiocGenerics rbind cbind

+##' @importFrom SummarizedExperiment Assays

+##' @name poplin-combine/subset

+##' @docType methods

+NULL

+

 ## Need to think about how to handle metadata of poplinData(x) and

 ## poplinReducedData(x) when data are combined

-

 ## poplin class cbind and rbind

-##' @export

-##' @importFrom BiocGenerics rbind cbind

-##' @importFrom SummarizedExperiment Assays

 setMethod("rbind", "poplin", function(..., deparse.level = 1) {

   old_validity <- S4Vectors:::disableValidity()

   if (!isTRUE(old_validity)) {

@@ -51,6 +104,7 @@ setMethod("rbind", "poplin", function(..., deparse.level = 1) {

                               check = FALSE)

 })

+##' @rdname poplin-combine/subset

 setMethod("cbind", "poplin", function(..., deparse.level = 1) {

   old_validity <- S4Vectors:::disableValidity()

   if (!isTRUE(old_validity)) {

@@ -3,15 +3,19 @@

 ##' The poplin class is designed to process LC/MS data. It is an extension of

 ##' the standard SummarizedExperiment class, and supports additional containers

 ##' for data processing results (e.g., normalization, imputation) via

-##' [poplinData] and dimension reduction results (PCA, PLS-DA) via

-##' [poplinReducedData]. A poplin object also can be created by coercing from a

+##' [poplin_data] and dimension reduction results (PCA, PLS-DA) via

+##' [poplin_reduced]. A poplin object also can be created by coercing from a

 ##' \linkS4class{SummarizedExperiment} object.

-##' 

+##'

 ##' @param intensity Peak intensity matrix where rows represent features and

 ##'   columns represent samples.

 ##' @param ... Arguments passed to the [SummarizedExperiment] constructor.

 ##' @return A poplin object

 ##' @author Jaehyun Joo

+##' @name poplin-class

+##' @usage

+##' ## Constructor

+##' poplin(intensity, ...)

 ##' @examples

 ##' nsamp <- 20

 ##' nfeature <- 1000

@@ -20,6 +24,37 @@

 ##' ## Coercion from an SummarizedExperiment object

 ##' as(se, "poplin")

 ##'

+NULL

+

+##' Internal poplin fields

+##'

+##' Methods to get or set internal fields in a \linkS4class{poplin} object.

+##' These methods are not intended to be used by end users of the \pkg{poplin}

+##' package.

+##'

+##' In the snippets below, \code{x} is a \linkS4class{poplin} object.

+##'

+##' \describe{

+##'

+##' \item{\code{poplinData(x)}, \code{poplinData(x) <- value}:}{ Returns a

+##' \linkS4class{DataFrame} of matrices containing one or more data processing

+##' results. \code{value} must be a \linkS4class{DataFrame} with the dimension

+##' equal to \code{dim(x)}. End users are supposed to interact with this field

+##' via [poplin_data]. }

+##'

+##' \item{\code{poplinReducedData(x), \code{poplinReducedData(x) <- value}}:}{

+##' Returns a \linkS4class{DataFrame} of matrices containing one or more

+##' dimension-reduced data. \code{value} must be a \linkS4class{DataFrame} with

+##' the dimension equal to \code{ncol(x)}. End users are supposed to interact

+##' with this field via [poplin_reduced]. }

+##'

+##' }

+##'

+##' @seealso [poplin_data], [poplin_reduced]

+##' @name poplin-internals

+NULL

+

+

 ##' @export

 ##' @import methods

 ##' @importFrom SummarizedExperiment SummarizedExperiment

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

 ##'

 ##' @section Getter methods:

 ##'

-##' Let \code{x} is a \linkS4class{poplin} object.

+##' In the code snippets below, \code{x} is a \linkS4class{poplin} object.

 ##'

 ##' \describe{

 ##' \item{\code{poplin_data_names(x)}:}{

@@ -51,18 +51,18 @@

 ##' }

 ##'

 ##' @return

-##' @name poplinData

+##' @name poplin_data

+NULL

+

 ##' @export

 setMethod("poplinData", "poplin", function(x) x@poplinData)

-##' @rdname poplinData

 ##' @export

 setReplaceMethod("poplinData", "poplin", function(x, value) {

   x@poplinData <- value

   x

 })

-##' @rdname poplinData

 ##' @importClassesFrom S4Vectors SimpleList

 ##' @export

 setMethod(

@@ -78,7 +78,6 @@ setMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setReplaceMethod(

   "poplin_data_list",

@@ -101,7 +100,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setMethod(

   "poplin_data_names",

@@ -111,7 +109,6 @@ setMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setReplaceMethod(

   "poplin_data_names",

@@ -129,7 +126,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setMethod(

   "poplin_data",

@@ -143,7 +139,6 @@ setMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setMethod(

   "poplin_data",

@@ -158,7 +153,6 @@ setMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setMethod(

   "poplin_data",

@@ -173,7 +167,6 @@ setMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setReplaceMethod(

   "poplin_data",

@@ -190,7 +183,6 @@ setReplaceMethod(

 )

-##' @rdname poplinData

 ##' @export

 setReplaceMethod(

   "poplin_data",

@@ -213,7 +205,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinData

 ##' @export

 setReplaceMethod(

   "poplin_data",

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

 ##'

 ##' @section Getter methods:

 ##'

-##' Let \code{x} is a \linkS4class{poplin} object.

+##' In the code snippets below, \code{x} is a \linkS4class{poplin} object.

 ##'

 ##' \describe{

 ##' \item{\code{poplin_reduced_names(x)}:}{

@@ -51,20 +51,20 @@

 ##' be removed.

 ##' }

 ##' }

-##' @name poplinReducedData

+##' @name poplin_reduced

 ##' @return

+NULL

+

 ##' @export

 setMethod("poplinReducedData", "poplin", function(x) x@poplinReducedData)

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod("poplinReducedData", "poplin", function(x, value) {

   x@poplinReducedData <- value

   x

 })

-##' @rdname poplinReducedData

 ##' @importClassesFrom S4Vectors SimpleList

 ##' @export

 setMethod(

@@ -79,7 +79,6 @@ setMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod(

   "poplin_reduced_list",

@@ -104,7 +103,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setMethod(

   "poplin_reduced_names",

@@ -114,7 +112,6 @@ setMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod(

   "poplin_reduced_names",

@@ -133,7 +130,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setMethod(

   "poplin_reduced",

@@ -147,7 +143,6 @@ setMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setMethod(

   "poplin_reduced",

@@ -162,7 +157,6 @@ setMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setMethod(

   "poplin_reduced",

@@ -177,7 +171,6 @@ setMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod(

   "poplin_reduced",

@@ -193,7 +186,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod(

   "poplin_reduced",

@@ -213,7 +205,6 @@ setReplaceMethod(

   }

 )

-##' @rdname poplinReducedData

 ##' @export

 setReplaceMethod(

   "poplin_reduced",

@@ -77,7 +77,7 @@ setMethod(

   "poplin_reduce_pca",

   "matrix",

   function(x, ncomp = 2, center = TRUE, scale = FALSE, ...) {

-    .poplin_impute_pca(x, ncomp = ncomp, center = center, scale = scale, ...)

+    .poplin_reduce_pca(x, ncomp = ncomp, center = center, scale = scale, ...)

   }

 )

@@ -85,7 +85,7 @@ setMethod(

 setMethod(

   "poplin_reduce_pca",

   "poplin",

-  function(x, poplin_in, poplin_out, ncomp = 2, center = 2, scale = FALSE, ...) {

+  function(x, poplin_in, poplin_out, ncomp = 2, center = TRUE, scale = FALSE, ...) {

     .reduced_extract_and_assign(x, .poplin_reduce_pca,

                                 poplin_in, poplin_out,

                                 ncomp = ncomp, center = center, scale = scale, ...)

@@ -109,7 +109,7 @@ setMethod(

 ##'

 ##' Jesse H. Krijthe (2015). Rtsne: T-Distributed Stochastic Neighbor Embedding

 ##' using a Barnes-Hut Implementation, URL: https://github.com/jkrijthe/Rtsne

-##' 

+##'

 ##' @param x A matrix or \linkS4class{poplin} object.

 ##' @param poplin_in Name of a data matrix to retrieve.

 ##' @param poplin_out Name of a data matrix to store.

@@ -127,7 +127,7 @@ setMethod(

   "poplin_reduce_tsne",

   "matrix",

   function(x, ncomp = 2, normalize = TRUE, ...) {

-    .poplin_impute_tsne(x, ncomp = ncomp, normalize = normalize, ...)

+    .poplin_reduce_tsne(x, ncomp = ncomp, normalize = normalize, ...)

   }

 )

@@ -157,7 +157,7 @@ setMethod(

 ##' @param method A dimension reduction method. Default is 'pca'.

 ##' @param poplin_in Name of a data matrix to retrieve.

 ##' @param poplin_out Name of a data matrix to store.

-##' @param y A factor vector for discrete outcome. 

+##' @param y A factor vector for discrete outcome.

 ##' @param ncomp Output dimensionality.

 ##' @param center A logical indicating mean-centering prior to PLS-DA.

 ##' @param scale A logical indicating unit variance scaling prior to PLS-DA.

@@ -171,7 +171,7 @@ setMethod(

   "poplin_reduce_plsda",

   "matrix",

   function(x, y, ncomp = 2, center = TRUE, scale = FALSE, ...) {

-    .poplin_impute_plsda(x, y = y, ncomp = ncomp,

+    .poplin_reduce_plsda(x, y = y, ncomp = ncomp,

                          center = center, scale = scale, ...)

   }

 )

@@ -188,7 +188,3 @@ setMethod(

                                 center = center, scale = scale, ...)

   }

 )

-

-

-

-

similarity index 80%

rename from man/poplin.Rd

rename to man/poplin-class.Rd

@@ -1,9 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/poplin.R

-\name{poplin}

-\alias{poplin}

+\name{poplin-class}

+\alias{poplin-class}

 \title{The poplin class}

 \usage{

+## Constructor

 poplin(intensity, ...)

 }

 \arguments{

@@ -19,8 +20,8 @@ A poplin object

 The poplin class is designed to process LC/MS data. It is an extension of

 the standard SummarizedExperiment class, and supports additional containers

 for data processing results (e.g., normalization, imputation) via

-\link{poplinData} and dimension reduction results (PCA, PLS-DA) via

-\link{poplinReducedData}. A poplin object also can be created by coercing from a

+\link{poplin_data} and dimension reduction results (PCA, PLS-DA) via

+\link{poplin_reduced}. A poplin object also can be created by coercing from a

 \linkS4class{SummarizedExperiment} object.

 }

 \examples{

new file mode 100644

@@ -0,0 +1,60 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/combine-methods.R

+\docType{methods}

+\name{poplin-combine/subset}

+\alias{poplin-combine/subset}

+\title{Combining or subsetting poplin objects}

+\description{

+Methods to combine multiple \linkS4class{poplin} objects by row or column,

+or to subset a \linkS4class{poplin} object by row or column.

+}

+\section{Combining}{

+

+

+In the code snippets below, \code{...} represents multiple

+\linkS4class{poplin} objects to be combined.

+

+\describe{

+\item{\code{rbind(..., deparse.level = 1)}:}{

+

+Take a sequence of poplin objects in \code{...} and combine by rows. Note

+that all objects in ... must have the exact same values for

+\link{poplin_data_list}. See \code{?}\link{rbind} for the interpretation of

+\code{deparse.level}.

+

+}

+\item{\code{cbind(..., deparse.level = 1)}:}{

+

+Take a sequence of poplin objects in \code{...} and combine by columns. Note

+that all objects in ... must have the same values of \link{poplin_reduced_names}.

+Dimension reduction results with the same name across the objects will be

+combined row-wise to create the corresponding entry in the output object.

+See \code{?}\link{cbind} for the interpretation of \code{deparse.level}.

+

+}

+}

+

+Refer to \code{help("SummarizedExperiment-class", package =

+"SummarizedExperiment")} for details on how \code{rowData}, \code{colData},

+and \code{metadata} are combined in the output object.

+}

+

+\section{Subsetting}{

+

+

+In the code snippets below, \code{x} is a \linkS4class{poplin}

+object.

+

+\describe{

+

+\item{\code{x[i, j]}, \code{x[i, j] <- value}:}{\code{i} and \code{j} are

+indices specifying the rows and columns to extract or replace. Indices can

+be a logical, integer, character vector, or empty (missing). \code{value}

+must be a poplin object with the dimension and assay elements consistent

+with the subset \code{x[i, j]} being replaced. \code{value} is also expected

+to have the same name and order of \link{poplin_data_names} (and

+\link{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.}

+

+}

+}

+

new file mode 100644

@@ -0,0 +1,32 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/poplin.R

+\name{poplin-internals}

+\alias{poplin-internals}

+\title{Internal poplin fields}

+\description{

+Methods to get or set internal fields in a \linkS4class{poplin} object.

+These methods are not intended to be used by end users of the \pkg{poplin}

+package.

+}

+\details{

+In the snippets below, \code{x} is a \linkS4class{poplin} object.

+

+\describe{

+

+\item{\code{poplinData(x)}, \code{poplinData(x) <- value}:}{ Returns a

+\linkS4class{DataFrame} of matrices containing one or more data processing

+results. \code{value} must be a \linkS4class{DataFrame} with the dimension

+equal to \code{dim(x)}. End users are supposed to interact with this field

+via \link{poplin_data}. }

+

+\item{\code{poplinReducedData(x), \code{poplinReducedData(x) <- value}}:}{

+Returns a \linkS4class{DataFrame} of matrices containing one or more

+dimension-reduced data. \code{value} must be a \linkS4class{DataFrame} with

+the dimension equal to \code{ncol(x)}. End users are supposed to interact

+with this field via \link{poplin_reduced}. }

+

+}

+}

+\seealso{

+\link{poplin_data}, \link{poplin_reduced}

+}

similarity index 61%

rename from man/poplinData.Rd

rename to man/poplin_data.Rd

@@ -1,44 +1,8 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/poplinData-methods.R

-\name{poplinData}

-\alias{poplinData}

-\alias{poplinData<-,poplin-method}

-\alias{poplin_data_list,poplin-method}

-\alias{poplin_data_list<-,poplin-method}

-\alias{poplin_data_names,poplin-method}

-\alias{poplin_data_names<-,poplin,character-method}

-\alias{poplin_data,poplin,numeric-method}

-\alias{poplin_data,poplin,character-method}

-\alias{poplin_data,poplin,missing-method}

-\alias{poplin_data<-,poplin,numeric-method}

-\alias{poplin_data<-,poplin,character-method}

-\alias{poplin_data<-,poplin,missing-method}

+\name{poplin_data}

+\alias{poplin_data}

 \title{Poplin data methods}

-\usage{

-\S4method{poplinData}{poplin}(x)

-

-\S4method{poplinData}{poplin}(x) <- value

-

-\S4method{poplin_data_list}{poplin}(x)

-

-\S4method{poplin_data_list}{poplin}(x, check_dimnames = TRUE, ...) <- value

-

-\S4method{poplin_data_names}{poplin}(x)

-

-\S4method{poplin_data_names}{poplin,character}(x) <- value

-

-\S4method{poplin_data}{poplin,numeric}(x, type)

-

-\S4method{poplin_data}{poplin,character}(x, type)

-

-\S4method{poplin_data}{poplin,missing}(x, type)

-

-\S4method{poplin_data}{poplin,numeric}(x, type, check_dimnames = TRUE, ...) <- value

-

-\S4method{poplin_data}{poplin,character}(x, type, check_dimnames = TRUE, ...) <- value

-

-\S4method{poplin_data}{poplin,missing}(x, type, check_dimnames = TRUE, ...) <- value

-}

 \value{

 }

@@ -50,7 +14,7 @@ sets involved in normalization, imputation, and transformation.

 \section{Getter methods}{

-Let \code{x} is a \linkS4class{poplin} object.

+In the code snippets below, \code{x} is a \linkS4class{poplin} object.

 \describe{

 \item{\code{poplin_data_names(x)}:}{

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

   poplin_in,

   poplin_out,

   ncomp = 2,

-  center = 2,

+  center = TRUE,

   scale = FALSE,

   ...

 )

similarity index 59%

rename from man/poplinReducedData.Rd

rename to man/poplin_reduced.Rd

@@ -1,44 +1,8 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/poplinReducedData-methods.R

-\name{poplinReducedData}

-\alias{poplinReducedData}

-\alias{poplinReducedData<-,poplin-method}

-\alias{poplin_reduced_list,poplin-method}

-\alias{poplin_reduced_list<-,poplin-method}

-\alias{poplin_reduced_names,poplin-method}

-\alias{poplin_reduced_names<-,poplin,character-method}

-\alias{poplin_reduced,poplin,numeric-method}

-\alias{poplin_reduced,poplin,character-method}

-\alias{poplin_reduced,poplin,missing-method}

-\alias{poplin_reduced<-,poplin,numeric-method}

-\alias{poplin_reduced<-,poplin,character-method}

-\alias{poplin_reduced<-,poplin,missing-method}

+\name{poplin_reduced}

+\alias{poplin_reduced}

 \title{Poplin dimension-reduced data methods}

-\usage{

-\S4method{poplinReducedData}{poplin}(x)

-

-\S4method{poplinReducedData}{poplin}(x) <- value

-

-\S4method{poplin_reduced_list}{poplin}(x)

-

-\S4method{poplin_reduced_list}{poplin}(x, check_samplenames = TRUE, ...) <- value

-

-\S4method{poplin_reduced_names}{poplin}(x)

-

-\S4method{poplin_reduced_names}{poplin,character}(x) <- value

-

-\S4method{poplin_reduced}{poplin,numeric}(x, type)

-

-\S4method{poplin_reduced}{poplin,character}(x, type)

-

-\S4method{poplin_reduced}{poplin,missing}(x, type)

-

-\S4method{poplin_reduced}{poplin,numeric}(x, type, check_samplenames = TRUE, ...) <- value

-

-\S4method{poplin_reduced}{poplin,character}(x, type, check_samplenames = TRUE, ...) <- value

-

-\S4method{poplin_reduced}{poplin,missing}(x, type, check_samplenames = TRUE, ...) <- value

-}

 \value{

 }

@@ -50,7 +14,7 @@ representation (e.g., PCA, PLS-DA) of LC/MS data sets.

 \section{Getter methods}{

-Let \code{x} is a \linkS4class{poplin} object.

+In the code snippets below, \code{x} is a \linkS4class{poplin} object.

 \describe{

 \item{\code{poplin_reduced_names(x)}:}{