@@ -22,7 +22,7 @@ S3method(summary,poplin.pca)

 S3method(summary,poplin.plsda)

 S3method(summary,poplin.tsne)

 export("poplinData<-")

-export("poplinReducedData<-")

+export("poplinReduced<-")

 export("poplin_data<-")

 export("poplin_data_list<-")

 export("poplin_data_names<-")

@@ -33,17 +33,17 @@ export(.get_poplinData_data_character)

 export(.get_poplinData_data_integer)

 export(.get_poplinData_data_missing)

 export(.get_poplinData_names)

-export(.get_poplinReducedData_data_character)

-export(.get_poplinReducedData_data_integer)

-export(.get_poplinReducedData_data_missing)

+export(.get_poplinReduced_data_character)

+export(.get_poplinReduced_data_integer)

+export(.get_poplinReduced_data_missing)

 export(.set_poplinData_data_character)

 export(.set_poplinData_data_integer)

 export(.set_poplinData_data_missing)

 export(.set_poplinData_datalist)

-export(.set_poplinReducedData_data_character)

-export(.set_poplinReducedData_data_integer)

-export(.set_poplinReducedData_data_missing)

-export(.set_poplinReducedData_datalist)

+export(.set_poplinReduced_data_character)

+export(.set_poplinReduced_data_integer)

+export(.set_poplinReduced_data_missing)

+export(.set_poplinReduced_datalist)

 export(.verify_and_extract_input)

 export(impute_knn)

 export(impute_pca)

@@ -59,7 +59,7 @@ export(normalize_sum)

 export(normalize_vsn)

 export(poplin)

 export(poplinData)

-export(poplinReducedData)

+export(poplinReduced)

 export(poplin_biplot)

 export(poplin_boxplot)

 export(poplin_corplot)

@@ -85,7 +85,7 @@ exportClasses(poplin.matrix)

 exportMethods("[")

 exportMethods("[<-")

 exportMethods("poplinData<-")

-exportMethods("poplinReducedData<-")

+exportMethods("poplinReduced<-")

 exportMethods("poplin_data<-")

 exportMethods("poplin_data_list<-")

 exportMethods("poplin_data_names<-")

@@ -94,7 +94,7 @@ exportMethods("poplin_reduced_list<-")

 exportMethods("poplin_reduced_names<-")

 exportMethods(coerce)

 exportMethods(poplinData)

-exportMethods(poplinReducedData)

+exportMethods(poplinReduced)

 exportMethods(poplin_data)

 exportMethods(poplin_data_list)

 exportMethods(poplin_data_names)

@@ -5,7 +5,7 @@ setClass(

   "poplin",

   slots = c(

     poplinData = "DataFrame",

-    poplinReducedData = "DataFrame"

+    poplinReduced = "DataFrame"

   ),

   contains = "SummarizedExperiment"

 )

@@ -2,7 +2,7 @@

 ## is more expensive, and generally best avoided.

 #################################################################################

-## poplinData and poplinReducedData

+## poplinData and poplinReduced

 #################################################################################

 ##' @export

@@ -19,14 +19,14 @@ setGeneric(

 ##' @export

 setGeneric(

-  "poplinReducedData",

-  function(x) standardGeneric("poplinReducedData")

+  "poplinReduced",

+  function(x) standardGeneric("poplinReduced")

 )

 ##' @export

 setGeneric(

-  "poplinReducedData<-",

-  function(x, value) standardGeneric("poplinReducedData<-")

+  "poplinReduced<-",

+  function(x, value) standardGeneric("poplinReduced<-")

 )

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

 ##' @importFrom SummarizedExperiment SummarizedExperiment

 .poplin_to_se_coldata <- function(x) {

-  SummarizedExperiment(colData = poplinReducedData(x))

+  SummarizedExperiment(colData = poplinReduced(x))

 }

 ##' @importFrom SummarizedExperiment Assays

@@ -56,7 +56,7 @@

 NULL

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

-## poplinReducedData(x) when data are combined

+## poplinReduced(x) when data are combined

 ## poplin class cbind and rbind

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

   old_validity <- S4Vectors:::disableValidity()

@@ -87,20 +87,20 @@ setMethod("rbind", "poplin", function(..., deparse.level = 1) {

     metadata(poplinData_all) <- list() # clean metadata; consistency with assay-via method

   })

   ## Utilize SE class for combining objects: see the SingleCellExperiment source

-  poplinReducedData_se <- lapply(args, function(x) .poplin_to_se_coldata(x))

+  poplinReduced_se <- lapply(args, function(x) .poplin_to_se_coldata(x))

   tryCatch({

-    poplinReducedData_all <- colData(do.call(rbind, poplinReducedData_se))

+    poplinReduced_all <- colData(do.call(rbind, poplinReduced_se))

   },

   error = function(err) {

     stop(

-      "failed to combine 'poplinReducedData' in 'rbind(<",

+      "failed to combine 'poplinReduced' in 'rbind(<",

       class(args[[1]]), ">)':\n  ", conditionMessage(err)

     )

   })

   ## Skip validity checks with check = FALSE for efficiency as modification

   ## cannot alter the validity of object

   BiocGenerics:::replaceSlots(out, poplinData = poplinData_all,

-                              poplinReducedData = poplinReducedData_all,

+                              poplinReduced = poplinReduced_all,

                               check = FALSE)

 })

@@ -129,18 +129,18 @@ setMethod("cbind", "poplin", function(..., deparse.level = 1) {

     )

   })

   tryCatch({

-    poplinReducedData_all <- do.call(rbind, lapply(args, poplinReducedData))

+    poplinReduced_all <- do.call(rbind, lapply(args, poplinReduced))

   },

   error = function(err) {

     stop(

-      "failed to combine 'poplinReducedData' in 'cbind(<",

+      "failed to combine 'poplinReduced' in 'cbind(<",

       class(args[[1]]), ">)':\n  ", conditionMessage(err)

     )

   })

   ## Skip validity checks with check = FALSE for efficiency as modification

   ## cannot alter the validity of object

   BiocGenerics:::replaceSlots(out, poplinData = poplinData_all,

-                              poplinReducedData = poplinReducedData_all,

+                              poplinReduced = poplinReduced_all,

                               check = FALSE)

 })

@@ -41,7 +41,7 @@ NULL

 ##' 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}:}{

+##' \item{\code{poplinReduced(x)}, \code{poplinReduced(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

@@ -52,8 +52,8 @@ NULL

 ##' @aliases

 ##' poplinData

 ##' poplinData<-

-##' poplinReducedData

-##' poplinReducedData<-

+##' poplinReduced

+##' poplinReduced<-

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

 ##' @name poplin-internals

 NULL

@@ -87,7 +87,7 @@ poplin <- function(intensity,  ...) {

     "poplin",

     se,

     poplinData = new("DFrame", nrows = nrow(se)),

-    poplinReducedData = new("DFrame", nrows = ncol(se))

+    poplinReduced = new("DFrame", nrows = ncol(se))

   )

 }

similarity index 87%

rename from R/poplinReducedData-internals.R

rename to R/poplinReduced-internals.R

@@ -1,29 +1,29 @@

-.get_poplinReducedData_names <- function(...) {

+.get_poplinReduced_names <- function(...) {

   .get_poplinData_names(...)

 }

-.set_poplinReducedData_names <- function(...) {

+.set_poplinReduced_names <- function(...) {

   .set_poplinData_names(...)

 }

 ##' @export

-.get_poplinReducedData_data_integer <- function(...) {

+.get_poplinReduced_data_integer <- function(...) {

   .get_poplinData_data_integer(...)

 }

 ##' @export

-.get_poplinReducedData_data_character <- function(...) {

+.get_poplinReduced_data_character <- function(...) {

   .get_poplinData_data_character(...)

 }

 ##' @export

-.get_poplinReducedData_data_missing <- function(...) {

+.get_poplinReduced_data_missing <- function(...) {

   .get_poplinData_data_missing(...)

 }

 ##' @export

-.set_poplinReducedData_data_integer <- function(x, type, value, get_slot,

+.set_poplinReduced_data_integer <- function(x, type, value, get_slot,

                                                 set_element_fun, funstr) {

   ## x <- updateObject(x)

@@ -53,7 +53,7 @@

 ##' @export

-.set_poplinReducedData_data_character <- function(x, type, value, get_slot,

+.set_poplinReduced_data_character <- function(x, type, value, get_slot,

                                                   set_element_fun, funstr) {

   ## x <- updateObject(x)

@@ -77,7 +77,7 @@

 }

 ##' @export

-.set_poplinReducedData_data_missing <- function(...) {

+.set_poplinReduced_data_missing <- function(...) {

   .set_poplinData_data_missing(...)

 }

@@ -85,7 +85,7 @@

 ##' @export

 ##' @importFrom methods as

 ##' @importFrom S4Vectors DataFrame I mcols mcols<- metadata metadata<-

-.set_poplinReducedData_datalist <- function(x, value, get_slot, set_element_fun,

+.set_poplinReduced_datalist <- function(x, value, get_slot, set_element_fun,

                                             funstr, name_pattern) {

   ## x <- updateObject(x)

similarity index 82%

rename from R/poplinReducedData-methods.R

rename to R/poplinReduced-methods.R

@@ -11,7 +11,7 @@

 ##' \describe{

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

 ##' Return the names of all dimension-reduced data sets stored in

-##' \code{x@poplinReducedData}.

+##' \code{x@poplinReduced}.

 ##' }

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

 ##' Retrieves a named \linkS4class{List} of matrices containing one or more

@@ -57,12 +57,12 @@

 NULL

 ##' @export

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

+setMethod("poplinReduced", "poplin", function(x) x@poplinReduced)

 ##' @export

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

-  x@poplinReducedData <- value

+setReplaceMethod("poplinReduced", "poplin", function(x, value) {

+  x@poplinReduced <- value

   x

 })

@@ -72,7 +72,7 @@ setMethod(

   "poplin_reduced_list",

   "poplin",

   function(x) {

-    value <- as(poplinReducedData(x), "SimpleList")

+    value <- as(poplinReduced(x), "SimpleList")

     for (i in seq_along(value)) {

       rownames(value[[i]]) <- colnames(x)

     }

@@ -95,10 +95,10 @@ setReplaceMethod(

       stop("'names(value)' contains duplicates. ",

            "Use different names for incoming data.")

     }

-    .set_poplinReducedData_datalist(

+    .set_poplinReduced_datalist(

       x, value,

-      get_slot = poplinReducedData,

-      set_element_fun = `poplinReducedData<-`,

+      get_slot = poplinReduced,

+      set_element_fun = `poplinReduced<-`,

       funstr = "poplin_reduced_list",

       name_pattern = "reduced")

   }

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

   "poplin_reduced_names",

   "poplin",

   function(x) {

-    .get_poplinReducedData_names(x, get_slot = poplinReducedData)

+    .get_poplinReduced_names(x, get_slot = poplinReduced)

   }

 )

@@ -122,10 +122,10 @@ setReplaceMethod(

       stop("'value' contains duplicates. ",

            "Use unique names.")

     }

-    .set_poplinReducedData_names(

+    .set_poplinReduced_names(

       x, value,

-      get_slot = poplinReducedData,

-      set_element_fun = `poplinReducedData<-`,

+      get_slot = poplinReduced,

+      set_element_fun = `poplinReduced<-`,

       name_pattern = "reduced"

     )

   }

@@ -136,9 +136,9 @@ setMethod(

   "poplin_reduced",

   c("poplin", "numeric"),

   function(x, type) {

-    .get_poplinReducedData_data_integer(

+    .get_poplinReduced_data_integer(

       x, type,

-      get_slot = poplinReducedData,

+      get_slot = poplinReduced,

       funstr = "poplin_reduced"

     )

   }

@@ -149,9 +149,9 @@ setMethod(

   "poplin_reduced",

   c("poplin", "character"),

   function(x, type) {

-    .get_poplinReducedData_data_character(

+    .get_poplinReduced_data_character(

       x, type,

-      get_slot = poplinReducedData,

+      get_slot = poplinReduced,

       funstr ="poplin_reduced",

       namestr = "poplin_reduced_names"

     )

@@ -163,7 +163,7 @@ setMethod(

   "poplin_reduced",

   c("poplin", "missing"),

   function(x, type) {

-    .get_poplinReducedData_data_missing(

+    .get_poplinReduced_data_missing(

       x,

       base_fun = poplin_reduced,

       name_fun = poplin_reduced_names,

@@ -180,10 +180,10 @@ setReplaceMethod(

     if (check_samplenames) {

       value <- .check_samplenames(x, value, fun = "poplin_reduced<-")

     }

-    .set_poplinReducedData_data_integer(

+    .set_poplinReduced_data_integer(

       x, type, value,

-      get_slot = poplinReducedData,

-      set_element_fun = `poplinReducedData<-`,

+      get_slot = poplinReduced,

+      set_element_fun = `poplinReduced<-`,

       funstr = "poplin_reduced"

     )

   }

@@ -201,10 +201,10 @@ setReplaceMethod(

     if (check_samplenames) {

       value <- .check_samplenames(x, value, fun = "poplin_reduced<-")

     }

-    .set_poplinReducedData_data_character(

+    .set_poplinReduced_data_character(

       x, type, value,

-      get_slot = poplinReducedData,

-      set_element_fun = `poplinReducedData<-`,

+      get_slot = poplinReduced,

+      set_element_fun = `poplinReduced<-`,

       funstr = "poplin_reduced"

     )

   }

@@ -215,7 +215,7 @@ setReplaceMethod(

   "poplin_reduced",

   c("poplin", "missing"),

   function(x, type, check_samplenames = TRUE, ..., value) {

-    .set_poplinReducedData_data_missing(

+    .set_poplinReduced_data_missing(

       x, value,

       base_fun = `poplin_reduced<-`,

       name_fun = poplin_reduced_names,

@@ -4,14 +4,14 @@ setMethod("[", c("poplin", "ANY", "ANY"), function(x, i, j, ..., drop = TRUE) {

     ii <- .get_subset_index(i, rownames(x))

     poplinData(x) <- poplinData(x)[ii, , drop = FALSE]

     ## if (length(reducedDataList(x)) != 0L) {

-    ##   message("Row-subsetting operation: 'poplinReducedData' slot was reset.")

+    ##   message("Row-subsetting operation: 'poplinReduced' slot was reset.")

     ## }

-    ## poplinReducedData(x) <- new("DFrame", nrows = ncol(x))

+    ## poplinReduced(x) <- new("DFrame", nrows = ncol(x))

   }

   if (!missing(j)) {

     jj <- .get_subset_index(j, colnames(x))

     poplinData(x) <- .subset_columns(x, jj, get_slot = poplinData)

-    poplinReducedData(x) <- poplinReducedData(x)[jj, , drop = FALSE]

+    poplinReduced(x) <- poplinReduced(x)[jj, , drop = FALSE]

   }

   callNextMethod()

 })

@@ -38,8 +38,8 @@ setReplaceMethod(

         })

         poplinData(x) <- poplinData_left

       }

-      ## message("Row-subsetting operation: 'poplinReducedData' slot was reset.")

-      ## poplinReducedData(x) <- new("DFrame", nrows = ncol(x))

+      ## message("Row-subsetting operation: 'poplinReduced' slot was reset.")

+      ## poplinReduced(x) <- new("DFrame", nrows = ncol(x))

     }

     if (!missing(j)) {

@@ -62,18 +62,18 @@ setReplaceMethod(

             conditionMessage(err))

         })

       }

-      poplinReducedData_left <- poplinReducedData(x)

-      poplinReducedData_right <- poplinReducedData(value)

+      poplinReduced_left <- poplinReduced(x)

+      poplinReduced_right <- poplinReduced(value)

       tryCatch({

-        poplinReducedData_left[jj, ] <- poplinReducedData_right

+        poplinReduced_left[jj, ] <- poplinReduced_right

       }, error=function(err) {

         stop(

-          "failed to replace 'poplinReducedData' in '<", class(x), ">[,j] <- value'\n",

+          "failed to replace 'poplinReduced' in '<", class(x), ">[,j] <- value'\n",

           conditionMessage(err))

       })

       poplinData(x) <- poplinData_left

-      poplinReducedData(x) <- poplinReducedData_left

+      poplinReduced(x) <- poplinReduced_left

     }

     callNextMethod()

 })

Binary files a/data/faahko_poplin.rda and b/data/faahko_poplin.rda differ

@@ -4,6 +4,8 @@

 \alias{poplin-internals}

 \alias{poplinData}

 \alias{poplinData<-}

+\alias{poplinReduced}

+\alias{poplinReduced<-}

 \title{Internal poplin fields}

 \description{

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

@@ -21,7 +23,7 @@ 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}:}{

+\item{\code{poplinReduced(x)}, \code{poplinReduced(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

@@ -17,7 +17,7 @@ In the code snippets below, \code{x} is a \linkS4class{poplin} object.

 \describe{

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

 Return the names of all dimension-reduced data sets stored in

-\code{x@poplinReducedData}.

+\code{x@poplinReduced}.

 }

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

 Retrieves a named \linkS4class{List} of matrices containing one or more

similarity index 100%

rename from tests/testthat/test-poplinRawData.R

rename to tests/testthat/test-poplinRaw.R

similarity index 100%

rename from tests/testthat/test-poplinReducedData.R

rename to tests/testthat/test-poplinReduced.R