-
Notifications
You must be signed in to change notification settings - Fork 34
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
deprecate longFormat and use longForm from BiocGenerics
- Loading branch information
Showing
10 changed files
with
266 additions
and
105 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| #' @name longFormat-deprecated | ||
| #' | ||
| #' @title Deprecated longFormat method | ||
| #' | ||
| #' @description The `longFormat` method is deprecated and will be removed in a | ||
| #' future release. Please use the `longForm` method instead. | ||
| #' | ||
| #' @details The `longFormat` "ANY" class method, works with classes such as | ||
| #' [`ExpressionSet`][Biobase::ExpressionSet] and | ||
| #' [`SummarizedExperiment`][SummarizedExperiment::SummarizedExperiment-class] as | ||
| #' well as `matrix` to provide a consistent long and skinny | ||
| #' [`DataFrame`][S4Vectors::DataFrame-class]. | ||
| #' | ||
| #' @section longFormat: | ||
| #' The 'longFormat' method takes data from the [`ExperimentList`] | ||
| #' in a `MultiAssayExperiment` and returns a uniform | ||
| #' `DataFrame`. The resulting DataFrame has columns indicating | ||
| #' primary, rowname, colname and value. This method can optionally include | ||
| #' columns of the MultiAssayExperiment colData named by `colDataCols` character | ||
| #' vector argument. (`MultiAssayExperiment` method only). The `i` argument | ||
| #' allows the user to specify the assay value for the | ||
| #' `SummarizedExperiment` assay function's `i` argument. | ||
| #' | ||
| #' @param object Any supported class object | ||
| #' | ||
| #' @param colDataCols A `character`, `logical`, or `numeric` | ||
| #' index for `colData` columns to be included | ||
| #' | ||
| #' @param i longFormat: The i-th assay in | ||
| #' `SummarizedExperiment`-like objects. A vector input is | ||
| #' supported in the case that the `SummarizedExperiment` object(s) has more | ||
| #' than one assay (default 1L), | ||
| #' renameColname: Either a `numeric` or `character` index | ||
| #' indicating the assay whose colnames are to be renamed | ||
| #' | ||
| #' @param ... Additional arguments. See details for more information. | ||
| #' | ||
| #' @importFrom BiocBaseUtils lifeCycle | ||
| #' | ||
| #' @aliases longFormat | ||
| #' @export | ||
| setGeneric( | ||
| "longFormat", | ||
| function(object, colDataCols = NULL, i = 1L, ...) | ||
| standardGeneric("longFormat") | ||
| ) | ||
|
|
||
| #' @rdname longFormat-deprecated | ||
| #' @exportMethod longFormat | ||
| setMethod( | ||
| "longFormat", "MultiAssayExperiment", | ||
| function(object, colDataCols = NULL, i = 1L, ...) { | ||
| if (any(.emptyAssays(experiments(object)))) | ||
| object <- .dropEmpty(object, warn = FALSE) | ||
|
|
||
| longDataFrame <- longFormat(experiments(object), i = i) | ||
|
|
||
| longDataFrame <- .mapOrderPrimary(longDataFrame, sampleMap(object)) | ||
|
|
||
| if (!is.null(colDataCols)) | ||
| longDataFrame <- | ||
| .matchAddColData(longDataFrame, colData(object), colDataCols) | ||
|
|
||
| as(longDataFrame, "DataFrame") | ||
| } | ||
| ) | ||
|
|
||
| #' @rdname longFormat-deprecated | ||
| #' @exportMethod longFormat | ||
| setMethod("longFormat", "ANY", function(object, colDataCols, i = 1L, ...) { | ||
| rowNAMES <- rownames(object) | ||
| if (is.null(rowNAMES)) rowNames <- as.character(seq_len(nrow(object))) | ||
|
|
||
| if (is(object, "ExpressionSet")) | ||
| object <- Biobase::exprs(object) | ||
| if (is(object, "SummarizedExperiment") || is(object, "RaggedExperiment")) | ||
| object <- assay(object, i = i) | ||
|
|
||
| BiocBaseUtils::checkInstalled("reshape2") | ||
|
|
||
| res <- reshape2::melt( | ||
| object, varnames = c("rowname", "colname"), value.name = "value" | ||
| ) | ||
| if (!is.character(res[["rowname"]])) | ||
| res[["rowname"]] <- as.character(res[["rowname"]]) | ||
| res | ||
| }) | ||
|
|
||
| #' @rdname longFormat-deprecated | ||
| #' @exportMethod longFormat | ||
| setMethod( | ||
| "longFormat", "ExperimentList", | ||
| function(object, colDataCols, i = 1L, ...) { | ||
| lifeCycle( | ||
| "longForm", package = "MultiAssayExperiment", title = "longFormat" | ||
| ) | ||
| samelength <- identical(length(object), length(i)) | ||
| if (!samelength && identical(length(i), 1L)) | ||
| i <- rep(i, length(object)) | ||
| res <- mapply( | ||
| function(obj, obname, idx) { | ||
| data.frame( | ||
| assay = obname, | ||
| longFormat(obj, i = idx), | ||
| stringsAsFactors = FALSE | ||
| ) | ||
| }, obj = object, obname = names(object), idx = i, SIMPLIFY = FALSE | ||
| ) | ||
|
|
||
| do.call( | ||
| function(...) rbind(..., make.row.names = FALSE), | ||
| res | ||
| ) | ||
| } | ||
| ) |
Oops, something went wrong.