Replace getExperiment* and testExperiment* functions with getCrossAss…

…ociation (#511)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.1
+Version: 1.13.2
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "felix.gm.ernst@outlook.com",

NAMESPACE

@@ -32,6 +32,7 @@ export(estimateFaith)
 export(estimateRichness)
 export(full_join)
 export(getBestDMNFit)
+export(getCrossAssociation)
 export(getDMN)
 export(getExperimentCrossAssociation)
 export(getExperimentCrossCorrelation)
@@ -145,6 +146,7 @@ exportMethods(estimateFaith)
 exportMethods(estimateRichness)
 exportMethods(full_join)
 exportMethods(getBestDMNFit)
+exportMethods(getCrossAssociation)
 exportMethods(getDMN)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)

NEWS

@@ -115,3 +115,4 @@ Changes in version 1.11.x
 
 Changes in version 1.13.x
 + Added new functions getMediation and addMediation
++ replace getExperiment* and testExperiment* functions with getCrossAssociation

R/deprecate.R

@@ -62,6 +62,86 @@ setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
 
 #' @rdname deprecate
 #' @export
+setGeneric("getExperimentCrossAssociation", signature = c("x"),
+           function(x, ...)
+               standardGeneric("getExperimentCrossAssociation"))
+
+#' @rdname deprecate
+#' @export
+setMethod("getExperimentCrossAssociation", 
+            signature = c(x = "MultiAssayExperiment"),
+            function(x, ...){
+                .Deprecated(msg = paste0("'getExperimentCrossAssociation' is ",
+                                        "deprecated. Use ", 
+                                        "'getCrossAssociation' instead."))
+                getCrossAssociation(x, ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("getExperimentCrossAssociation", signature = "SummarizedExperiment",
+          function(x, ...){
+              .Deprecated(msg = paste0("'getExperimentCrossAssociation' is ",
+                                       "deprecated. Use ", 
+                                       "'getCrossAssociation' instead."))
+              getCrossAssociation(x, ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("testExperimentCrossAssociation", signature = c("x"),
+           function(x, ...)
+               standardGeneric("testExperimentCrossAssociation"))
+
+#' @rdname deprecate
+#' @export
+setMethod("testExperimentCrossAssociation", signature = c(x = "ANY"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'testExperimentCrossAssociation' is ",
+                                       "deprecated. Use ", 
+                                       "'getCrossAssociation' instead."))
+              getCrossAssociation(x, test_significance = TRUE, ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("testExperimentCrossCorrelation", signature = c("x"),
+           function(x, ...)
+               standardGeneric("testExperimentCrossCorrelation"))
+
+#' @rdname deprecate
+#' @export
+setMethod("testExperimentCrossCorrelation", signature = c(x = "ANY"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'testExperimentCrossCorrelation' is ",
+                                       "deprecated. Use ", 
+                                       "'getCrossAssociation' instead."))
+              getCrossAssociation(x, test_significance = TRUE, ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("getExperimentCrossCorrelation", signature = c("x"),
+           function(x, ...)
+               standardGeneric("getExperimentCrossCorrelation"))
+
+#' @rdname deprecate
+#' @export
+setMethod("getExperimentCrossCorrelation", signature = c(x = "ANY"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'getExperimentCrossCorrelation' is ",
+                                       "deprecated. Use ", 
+                                       "'getCrossAssociation' instead."))
+              getCrossAssociation(x, ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export              
 setGeneric("mergeFeaturesByPrevalence", signature = "x",
            function(x, ...)
                standardGeneric("mergeFeaturesByPrevalence"))

R/getExperimentCrossAssociation.R → R/getCrossAssociation.R

@@ -89,6 +89,7 @@
 #'    
 #' @param test_significance A single boolean value for selecting whether to test
 #'    statistical significance of associations.
+#'    (By default: \code{test_significance = FALSE})
 #'    
 #' @param show_warnings A single boolean value for selecting whether to show warnings
 #'    that might occur when correlations and p-values are calculated.
@@ -111,24 +112,24 @@
 #'    }
 #'    
 #' @details
-#' These functions calculates associations between features of two experiments. 
-#' \code{getExperimentCrossAssociation} calculates only associations by default.
-#' \code{testExperimentCrossAssociation} calculates also significance of 
-#' associations.
+#' The function \code{getCrossAssociation} calculates associations between 
+#' features of two experiments. By default, it not only computes associations 
+#' but also tests their significance. If desired, setting 
+#' \code{test_significance} to FALSE disables significance calculation.
 #' 
 #' We recommend the non-parametric Kendall's tau as the default method for association 
 #' analysis. Kendall's tau has desirable statistical properties and robustness at lower 
 #' sample sizes. Spearman rank correlation can provide faster solutions when 
 #' running times are critical.
 #'
 #' @return 
-#' These functions return associations in table or matrix format. In table format,
+#' This function returns associations in table or matrix format. In table format,
 #' returned value is a data frame that includes  features and associations 
 #' (and p-values) in columns. In matrix format, returned value is a one matrix
 #' when only associations are calculated. If also significances are tested, then
 #' returned value is a list of matrices.
 #'
-#' @name getExperimentCrossAssociation
+#' @name getCrossAssociation
 #' @export
 #'
 #' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
@@ -147,7 +148,7 @@
 #' mae[[1]] <- transformAssay(mae[[1]], method = "rclr")
 #' 
 #' # Calculate cross-correlations
-#' result <- getExperimentCrossAssociation(mae, method = "pearson", assay.type2 = "nmr")
+#' result <- getCrossAssociation(mae, method = "pearson", assay.type2 = "nmr")
 #' # Show first 5 entries
 #' head(result, 5)
 #' 
@@ -156,47 +157,44 @@
 #' # Transform data
 #' altExp(mae[[1]], "Phylum") <- transformAssay(altExp(mae[[1]], "Phylum"), method = "relabundance")
 #' # When mode = "matrix", the return value is a matrix
-#' result <- getExperimentCrossAssociation(mae, experiment2 = 2, 
+#' result <- getCrossAssociation(mae, experiment2 = 2, 
 #'                                         assay.type1 = "relabundance", assay.type2 = "nmr",
 #'                                         altexp1 = "Phylum", 
 #'                                         method = "pearson", mode = "matrix")
 #' # Show first 5 entries
 #' head(result, 5)
 #' 
-#' # testExperimentCorrelation additionally returns significances
+#' # If test_significance = TRUE, then getCrossAssociation additionally returns 
+#' # significances
 #' # filter_self_correlations = TRUE filters self correlations
 #' # p_adj_threshold can be used to filter those features that do not
 #' # have any correlations whose p-value is lower than the threshold
-#' result <- testExperimentCrossAssociation(mae[[1]], experiment2 = mae[[1]], method = "pearson",
+#' result <- getCrossAssociation(mae[[1]], experiment2 = mae[[1]], method = "pearson",
 #'                                          filter_self_correlations = TRUE,
-#'                                          p_adj_threshold = 0.05)
+#'                                          p_adj_threshold = 0.05,
+#'                                          test_significance = TRUE)
 #' # Show first 5 entries
 #' head(result, 5)
-#' 
-#' # getExperimentCrossAssociation also returns significances when 
-#' # test_significance = TRUE
-#' # Warnings can be suppressed by using show_warnings = FALSE
-#' result <- getExperimentCrossAssociation(mae[[1]], experiment2 = mae[[2]], method = "pearson",
-#'                                         assay.type2 = "nmr",
-#'                                         mode = "matrix", test_significance = TRUE,
-#'                                         show_warnings = FALSE)
 #'                                         
 #' # Returned value is a list of matrices
 #' names(result)
 #' 
 #' # Calculate Bray-Curtis dissimilarity between samples. If dataset includes
 #' # paired samples, you can use paired = TRUE.
-#' result <- getExperimentCrossAssociation(mae[[1]], mae[[1]], MARGIN = 2, paired = FALSE,
-#'                                         association_FUN = vegan::vegdist, method = "bray")
+#' result <- getCrossAssociation(mae[[1]], mae[[1]], MARGIN = 2, paired = FALSE,
+#'                                         association_FUN = vegan::vegdist, 
+#'                                         method = "bray")
 #'                                         
 #' 
 #' # If experiments are equal and measure is symmetric (e.g., taxa1 vs taxa2 == taxa2 vs taxa1),
 #' # it is possible to speed-up calculations by calculating association only for unique
 #' # variable-pairs. Use "symmetric" to choose whether to measure association for only
 #' # other half of of variable-pairs.
-#' result <- getExperimentCrossAssociation(mae, experiment1 = "microbiota", experiment2 = "microbiota", 
-#'                                         assay.type1 = "counts", assay.type2 = "counts",
-#'                                         symmetric = TRUE)
+#' result <- getCrossAssociation(mae, experiment1 = "microbiota", 
+#'                                  experiment2 = "microbiota", 
+#'                                  assay.type1 = "counts", 
+#'                                  assay.type2 = "counts",
+#'                                  symmetric = TRUE)
 #' 
 #' # For big data sets, the calculations might take a long time.
 #' # To speed them up, you can take a random sample from the data. 
@@ -205,30 +203,29 @@
 #' sample_size <- 0.3
 #' tse <- mae[[1]]
 #' tse_sub <- tse[ sample( seq_len( nrow(tse) ), sample_size * nrow(tse) ), ]
-#' result <- testExperimentCrossAssociation(tse_sub)
+#' result <- getCrossAssociation(tse_sub)
 #' 
 #' # It is also possible to choose variables from colData and calculate association
 #' # between assay and sample metadata or between variables of sample metadata
 #' mae[[1]] <- estimateDiversity(mae[[1]])
 #' # colData_variable works similarly to assay.type. Instead of fetching an assay
 #' # named assay.type from assay slot, it fetches a column named colData_variable
 #' # from colData.
-#' result <- getExperimentCrossAssociation(mae[[1]], assay.type1 = "counts", 
-#'                                         colData_variable2 = c("shannon", "coverage"))
+#' result <- getCrossAssociation(mae[[1]], assay.type1 = "counts", 
+#'                                  colData_variable2 = c("shannon", "coverage"),
+#'                                  test_significance = TRUE)
 #'                                         
 NULL
 
-#' @rdname getExperimentCrossAssociation
-#' @aliases getExperimentCrossCorrelation
+#' @rdname getCrossAssociation
 #' @export
-setGeneric("getExperimentCrossAssociation", signature = c("x"),
+setGeneric("getCrossAssociation", signature = c("x"),
            function(x, ...)
-               standardGeneric("getExperimentCrossAssociation"))
+               standardGeneric("getCrossAssociation"))
 
-#' @rdname getExperimentCrossAssociation
-#' @aliases getExperimentCrossCorrelation
+#' @rdname getCrossAssociation
 #' @export
-setMethod("getExperimentCrossAssociation", signature = c(x = "MultiAssayExperiment"),
+setMethod("getCrossAssociation", signature = c(x = "MultiAssayExperiment"),
     function(x,
            experiment1 = 1,
            experiment2 = 2,
@@ -277,12 +274,11 @@ setMethod("getExperimentCrossAssociation", signature = c(x = "MultiAssayExperime
     }
 )
 
-#' @rdname getExperimentCrossAssociation
-#' @aliases getExperimentCrossCorrelation
+#' @rdname getCrossAssociation
 #' @importFrom MultiAssayExperiment MultiAssayExperiment ExperimentList
 #' @importFrom SingleCellExperiment altExps
 #' @export
-setMethod("getExperimentCrossAssociation", signature = "SummarizedExperiment",
+setMethod("getCrossAssociation", signature = "SummarizedExperiment",
     function(x, experiment2 = x, ...){
         ############################## INPUT CHECK #############################
         # If y is  SE or TreeSE object
@@ -341,54 +337,6 @@ setMethod("getExperimentCrossAssociation", signature = "SummarizedExperiment",
     }
 )
 
-#' @rdname getExperimentCrossAssociation
-#' @aliases testExperimentCrossCorrelation
-#' @export
-setGeneric("testExperimentCrossAssociation", signature = c("x"),
-           function(x, ...)
-               standardGeneric("testExperimentCrossAssociation"))
-
-#' @rdname getExperimentCrossAssociation
-#' @aliases testExperimentCrossCorrelation
-#' @export
-setMethod("testExperimentCrossAssociation", signature = c(x = "ANY"),
-          function(x, ...){
-              getExperimentCrossAssociation(x, test_significance = TRUE, ...)
-          }
-)
-
-############################# Methods for aliases ##############################
-#' @rdname getExperimentCrossAssociation
-#' @aliases testExperimentCrossAssociation
-#' @export
-setGeneric("testExperimentCrossCorrelation", signature = c("x"),
-           function(x, ...)
-               standardGeneric("testExperimentCrossCorrelation"))
-
-#' @rdname getExperimentCrossAssociation
-#' @aliases testExperimentCrossAssociation
-#' @export
-setMethod("testExperimentCrossCorrelation", signature = c(x = "ANY"),
-          function(x, ...){
-              getExperimentCrossAssociation(x, test_significance = TRUE, ...)
-          }
-)
-
-#' @rdname getExperimentCrossAssociation
-#' @aliases getExperimentCrossAssociation
-#' @export
-setGeneric("getExperimentCrossCorrelation", signature = c("x"),
-           function(x, ...)
-               standardGeneric("getExperimentCrossCorrelation"))
-
-#' @rdname getExperimentCrossAssociation
-#' @aliases getExperimentCrossAssociation
-#' @export
-setMethod("getExperimentCrossCorrelation", signature = c(x = "ANY"),
-          function(x, ...){
-              getExperimentCrossAssociation(x, ...)
-          }
-)
 ############################## MAIN FUNCTIONALITY ##############################
 # This function includes all the main functionality.
 #' @importFrom S4Vectors unfactor