Browse code

Set aliases for poplin internal document.

Jaehyun Joo authored on 22/12/2021 03:10:57
Showing 8 changed files

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@@ -15,6 +15,7 @@ RoxygenNote: 7.1.2
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 biocViews:
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 Imports: 
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     BiocGenerics,
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+    rlang,
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     ggplot2,
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     heatmaply,
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     methods,
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@@ -22,12 +23,14 @@ Imports:
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     stats
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 Suggests:
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     limma,
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+    Biobase,
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     missForest,
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     hexbin,
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     Rtsne,
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     vsn,
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     VIM,
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     pcaMethods,
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+    pls,
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     testthat (>= 3.0.0)
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 Depends: 
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     R (>= 3.6.0),
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@@ -45,26 +45,17 @@ export(.set_poplinReducedData_data_integer)
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 export(.set_poplinReducedData_data_missing)
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 export(.set_poplinReducedData_datalist)
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 export(.verify_and_extract_input)
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-export(impute_halfmin)
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 export(impute_knn)
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-export(impute_mean)
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-export(impute_median)
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 export(impute_pca)
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 export(impute_randomforest)
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 export(impute_simple)
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-export(normalize_auto)
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 export(normalize_cyclicloess)
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-export(normalize_euclidean)
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-export(normalize_level)
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 export(normalize_mad)
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 export(normalize_mean)
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 export(normalize_median)
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-export(normalize_pareto)
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 export(normalize_pqn)
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-export(normalize_range)
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 export(normalize_scale)
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 export(normalize_sum)
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-export(normalize_vast)
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 export(normalize_vsn)
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 export(poplin)
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 export(poplinData)
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@@ -142,12 +142,6 @@ setGeneric(
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   function(x, ...) standardGeneric("normalize_mad")
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 )
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-##' @export
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-setGeneric(
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-  "normalize_euclidean",
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-  function(x, ...) standardGeneric("normalize_euclidean")
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-)
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-
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 ##' @export
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 setGeneric(
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   "normalize_cyclicloess",
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@@ -160,36 +154,6 @@ setGeneric(
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   function(x, ...) standardGeneric("normalize_vsn")
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 )
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-##' @export
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-setGeneric(
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-  "normalize_auto",
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-  function(x, ...) standardGeneric("normalize_auto")
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-)
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-
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-##' @export
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-setGeneric(
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-  "normalize_range",
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-  function(x, ...) standardGeneric("normalize_range")
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-)
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-
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-##' @export
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-setGeneric(
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-  "normalize_pareto",
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-  function(x, ...) standardGeneric("normalize_pareto")
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-)
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-
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-##' @export
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-setGeneric(
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-  "normalize_vast",
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-  function(x, ...) standardGeneric("normalize_vast")
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-)
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-
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-##' @export
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-setGeneric(
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-  "normalize_level",
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-  function(x, ...) standardGeneric("normalize_level")
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-)
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-
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 ##' @export
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 setGeneric(
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   "normalize_scale",
... ...
@@ -213,24 +177,6 @@ setGeneric(
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   function(x, ...) standardGeneric("impute_knn")
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 )
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-##' @export
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-setGeneric(
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-  "impute_halfmin",
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-  function(x, ...) standardGeneric("impute_halfmin")
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-)
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-
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-##' @export
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-setGeneric(
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-  "impute_median",
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-  function(x, ...) standardGeneric("impute_median")
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-)
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-
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-##' @export
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-setGeneric(
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-  "impute_mean",
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-  function(x, ...) standardGeneric("impute_mean")
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-)
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-
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 ##' @export
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 setGeneric(
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   "impute_simple",
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@@ -13,14 +13,14 @@
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 ##'
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 ##' Take a sequence of poplin objects in \code{...} and combine by rows. Note
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 ##' that all objects in ... must have the exact same values for
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-##' [poplin_data_list]. See \code{?}[rbind] for the interpretation of
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+##' \code{poplin_data_list}. See \code{?}[rbind] for the interpretation of
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 ##' \code{deparse.level}.
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 ##'
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 ##' }
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 ##' \item{\code{cbind(..., deparse.level = 1)}:}{
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 ##'
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 ##' Take a sequence of poplin objects in \code{...} and combine by columns. Note
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-##' that all objects in ... must have the same values of [poplin_reduced_names].
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+##' that all objects in ... must have the same values of \code{poplin_reduced_names}.
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 ##' Dimension reduction results with the same name across the objects will be
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 ##' combined row-wise to create the corresponding entry in the output object.
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 ##' See \code{?}[cbind] for the interpretation of \code{deparse.level}.
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@@ -44,8 +44,8 @@
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 ##' be a logical, integer, character vector, or empty (missing). \code{value}
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 ##' must be a poplin object with the dimension and assay elements consistent
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 ##' with the subset \code{x[i, j]} being replaced. \code{value} is also expected
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-##' to have the same name and order of [poplin_data_names] (and
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-##' [poplin_reduced_names] as well if \code{j} is specified) as \code{x}.}
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+##' to have the same name and order of \code{poplin_data_names} (and
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+##' \code{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.}
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 ##'
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 ##' }
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 ##'
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@@ -165,6 +165,9 @@
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   if (!requireNamespace("vsn", quietly = TRUE)) {
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     stop("Package 'vsn' is required. Please install and try again.")
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   }
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+  if (!requireNamespace("Biobase", quietly = TRUE)) {
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+    stop("Package 'Biobase' is required. Please install and try again.")
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+  }
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   out <- suppressMessages(vsn::vsnMatrix(x = x, ...))
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   if (meanSdPlot) {
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     if (!requireNamespace("hexbin", quietly = TRUE)) {
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@@ -49,6 +49,11 @@ NULL
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 ##'
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 ##' }
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 ##'
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+##' @aliases
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+##' poplinData
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+##' poplinData<-
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+##' poplinReducedData
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+##' poplinReducedData<-
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 ##' @seealso [poplin_data], [poplin_reduced]
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 ##' @name poplin-internals
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 NULL
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@@ -19,14 +19,14 @@ In the code snippets below, \code{...} represents multiple
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 Take a sequence of poplin objects in \code{...} and combine by rows. Note
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 that all objects in ... must have the exact same values for
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-\link{poplin_data_list}. See \code{?}\link{rbind} for the interpretation of
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+\code{poplin_data_list}. See \code{?}\link{rbind} for the interpretation of
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 \code{deparse.level}.
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 }
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 \item{\code{cbind(..., deparse.level = 1)}:}{
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 Take a sequence of poplin objects in \code{...} and combine by columns. Note
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-that all objects in ... must have the same values of \link{poplin_reduced_names}.
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+that all objects in ... must have the same values of \code{poplin_reduced_names}.
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 Dimension reduction results with the same name across the objects will be
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 combined row-wise to create the corresponding entry in the output object.
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 See \code{?}\link{cbind} for the interpretation of \code{deparse.level}.
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@@ -52,8 +52,8 @@ indices specifying the rows and columns to extract or replace. Indices can
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 be a logical, integer, character vector, or empty (missing). \code{value}
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 must be a poplin object with the dimension and assay elements consistent
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 with the subset \code{x[i, j]} being replaced. \code{value} is also expected
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-to have the same name and order of \link{poplin_data_names} (and
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-\link{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.}
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+to have the same name and order of \code{poplin_data_names} (and
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+\code{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.}
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 }
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 }
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@@ -2,6 +2,8 @@
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 % Please edit documentation in R/poplin.R
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 \name{poplin-internals}
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 \alias{poplin-internals}
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+\alias{poplinData}
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+\alias{poplinData<-}
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 \title{Internal poplin fields}
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 \description{
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 Methods to get or set internal fields in a \linkS4class{poplin} object.