added checks, ttest and wilcoxon

.Rbuildignore

@@ -4,3 +4,5 @@
 ^README\.Rmd$
 ^\.github$
 ^codecov\.yml$
+^pkgdown$
+^README\.html$

DESCRIPTION

@@ -15,17 +15,24 @@ BugReports: https://github.com/microbiome/daa/issues/
 biocViews: Software, Microbiome
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
-    R (>= 4.5.0)
+    R (>= 4.5.0),
+    mia
 Imports:
-    dplyr
+    dplyr,
+    methods,
+    miaViz,
+    purrr,
+    rstatix,
+    S4Vectors,
+    SingleCellExperiment,
+    SummarizedExperiment
 Suggests:
     BiocStyle,
     knitr,
-    RefManageR,
+    MultiAssayExperiment,
     rmarkdown,
-    sessioninfo,
     testthat
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -1,2 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
+export(addTtest)
+export(addWilcoxon)
+export(getTtest)
+export(getWilcoxon)
+exportMethods(addTtest)
+exportMethods(addWilcoxon)
+exportMethods(getTtest)
+exportMethods(getWilcoxon)
+importFrom(S4Vectors,DataFrame)
+importFrom(SingleCellExperiment,altExp)
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
+importFrom(dplyr,across)
+importFrom(dplyr,all_of)
+importFrom(dplyr,arrange)
+importFrom(dplyr,group_split)
+importFrom(methods,callNextMethod)
+importFrom(mia,meltSE)
+importFrom(purrr,map_df)
+importFrom(rstatix,adjust_pvalue)
+importFrom(rstatix,t_test)
+importFrom(rstatix,wilcox_test)
+importFrom(stats,as.formula)

R/AllGenerics.R

@@ -0,0 +1,25 @@
+# This file contains all the generics
+
+#' @rdname getWilcoxon
+#' @export
+setGeneric( "getWilcoxon", signature = "x", function ( x, ... ){
+    standardGeneric("getWilcoxon")
+})
+
+#' @rdname getWilcoxon
+#' @export
+setGeneric( "addWilcoxon", signature = "x", function ( x, ... ){
+    standardGeneric("addWilcoxon")
+})
+
+#' @rdname getTtest
+#' @export
+setGeneric( "getTtest", signature = "x", function ( x, ... ){
+    standardGeneric("getTtest")
+})
+
+#' @rdname getTtest
+#' @export
+setGeneric( "addTtest", signature = "x", function ( x, ... ){
+    standardGeneric("addTtest")
+})

R/getTtest.R

@@ -0,0 +1,149 @@
+#' @name
+#' getTtest
+#'
+#' @title
+#' Perform t-test
+#'
+#' @description
+#' These functions perform t-test to compare values between two groups.
+#'
+#' @details
+#' By default, Welch's t-test is used which does not assume equal variances.
+#' Set \code{var.equal = TRUE} for Student's t-test.
+#'
+#' Specify exactly one of \code{assay.type}, \code{row.var}, or \code{col.var}
+#' to define the values to test.
+#'
+#' @return
+#' \code{getTtest} returns a \code{DataFrame} with test results.
+#' \code{addTtest} returns \code{x} with results added to \code{rowData(x)}.
+#'
+#' @param x A \code{SummarizedExperiment} object.
+#'
+#' @param assay.type \code{Character scalar} or \code{NULL}. Specifies assay to
+#' test. Tests are run per feature. (Default: \code{NULL})
+#'
+#' @param row.var \code{Character scalar} or \code{NULL}. Specifies variable
+#' from \code{rowData(x)} to test. (Default: \code{NULL})
+#'
+#' @param col.var \code{Character scalar} or \code{NULL}. Specifies variable
+#' from \code{colData(x)} to test. (Default: \code{NULL})
+#'
+#' @param formula \code{formula}. A formula specifying the grouping variable,
+#' e.g., \code{~ SampleType}. The RHS specifies the comparison groups.
+#' For >2 levels, pairwise comparisons are performed.
+#'
+#' @param split.by \code{Character vector} or \code{NULL}. Columns to split by.
+#' Tests are run separately for each combination. (Default: \code{NULL})
+#'
+#' @param pair.by \code{Character scalar} or \code{NULL}. Column for pairing
+#' samples in paired tests. (Default: \code{NULL})
+#'
+#' @param features \code{Character vector} or \code{NULL}. Specific features
+#' to test when using \code{assay.type}. (Default: \code{NULL})
+#'
+#' @param var.equal \code{Logical scalar}. Assume equal variances?
+#' (Default: \code{FALSE})
+#'
+#' @param p.adjust.method \code{Character scalar}. Method for p-value
+#' adjustment. (Default: \code{"fdr"})
+#'
+#' @param name \code{Character scalar}. Column name prefix for results.
+#' (Default: \code{"ttest"})
+#'
+#' @param ... Additional arguments passed to \code{rstatix::t_test}.
+#'
+#' @examples
+#' data(GlobalPatterns, package = "mia")
+#' tse <- GlobalPatterns
+#' tse <- tse[1:50, tse$SampleType %in% c("Feces", "Skin")]
+#'
+#' # Test assay values (per feature)
+#' res <- getTtest(tse, assay.type = "counts", formula = ~SampleType)
+#'
+#' # Test colData variable (e.g., alpha diversity)
+#' tse <- mia::addAlpha(tse, index = "shannon_diversity")
+#' res <- getTtest(tse, col.var = "shannon_diversity", formula = ~SampleType)
+#'
+#' @seealso
+#' \code{\link[rstatix:t_test]{rstatix::t_test}},
+#' \code{\link[daa:getWilcoxon]{getWilcoxon}}
+#'
+#' @export
+NULL
+
+#' @rdname getTtest
+#' @export
+#' @importFrom SingleCellExperiment altExp
+#' @importFrom methods callNextMethod
+setMethod("getTtest", "SingleCellExperiment", function (x, ... ){
+    x <- .check_and_get_altExp(x, ...)
+    res <- callNextMethod(x, ...)
+    return(res)
+})
+
+#' @rdname getTtest
+#' @export
+#' @importFrom SummarizedExperiment assay colData rowData
+#' @importFrom rstatix t_test adjust_pvalue
+#' @importFrom S4Vectors DataFrame
+setMethod(
+    "getTtest", "SummarizedExperiment",
+    function (x, assay.type = NULL, row.var = NULL, col.var = NULL,
+             formula, split.by = NULL, pair.by = NULL, features = NULL,
+             var.equal = FALSE, p.adjust.method = "fdr", ... ){
+        ############################# Input check ##############################
+        group <- .check_input(
+            x, assay.type, row.var, col.var, formula,
+            split.by, pair.by, features
+        )
+        if( !.is_a_bool(var.equal) ){
+            stop("'var.equal' must be TRUE or FALSE.", call. = FALSE)
+        }
+        ########################### Input check end ############################
+        # Get y variable name (the column to test)
+        y <- c(assay.type, row.var, col.var)
+        # Get data based on source
+        df <- .get_data(
+            x, assay.type, row.var, col.var, group,
+            split.by, pair.by, features
+        )
+        # Run tests
+        paired <- !is.null(pair.by)
+        res <- .run_ttest(
+            df, y, group, split.by, paired, var.equal,
+            p.adjust.method, features, ...
+        )
+        return(res)
+    }
+)
+
+#' @rdname getTtest
+#' @export
+setMethod(
+    "addTtest", "SummarizedExperiment",
+    function (x, name = "ttest", ... ){
+        if( !.is_non_empty_string(name) ){
+            stop("'name' must be a single character value.", call. = FALSE)
+        }
+        res <- getTtest(x, ...)
+        x <- .add_values_to_colData(x, list(res$p.adj), paste0(name, "_padj"),
+            MARGIN = 1
+        )
+        return(x)
+    }
+)
+
+################################################################################
+# Internal function using .calc_daa engine
+################################################################################
+
+#' @importFrom rstatix t_test
+.run_ttest <- function (df, y, group, split.by, paired, var.equal,
+                       p.adjust.method, features = NULL, ... ){
+    .calc_daa(
+        df = df, y = y, group = group, split.by = split.by,
+        paired = paired, FUN = rstatix::t_test,
+        p.adjust.method = p.adjust.method, features = features, var.equal = var.equal, ...
+    )
+}

R/getWilcoxon.R

@@ -0,0 +1,144 @@
+#' @name
+#' getWilcoxon
+#'
+#' @title
+#' Perform Wilcoxon rank-sum test
+#'
+#' @description
+#' These functions perform Wilcoxon rank-sum test (Mann-Whitney U) to compare
+#' values between two groups.
+#'
+#' @details
+#' The Wilcoxon rank-sum test is a non-parametric test used to compare two
+#' independent groups. It is suitable when data does not meet normality
+#' assumptions.
+#'
+#' Specify exactly one of \code{assay.type}, \code{row.var}, or \code{col.var}
+#' to define the values to test.
+#'
+#' @return
+#' \code{getWilcoxon} returns a \code{DataFrame} with test results.
+#' \code{addWilcoxon} returns \code{x} with results added to \code{rowData(x)}.
+#'
+#' @param x A \code{SummarizedExperiment} object.
+#'
+#' @param assay.type \code{Character scalar} or \code{NULL}. Specifies assay to
+#' test. Tests are run per feature. (Default: \code{NULL})
+#'
+#' @param row.var \code{Character scalar} or \code{NULL}. Specifies variable
+#' from \code{rowData(x)} to test. (Default: \code{NULL})
+#'
+#' @param col.var \code{Character scalar} or \code{NULL}. Specifies variable
+#' from \code{colData(x)} to test. (Default: \code{NULL})
+#'
+#' @param formula \code{formula}. A formula specifying the grouping variable,
+#' e.g., \code{~ SampleType}. The RHS specifies the comparison groups.
+#' For >2 levels, pairwise comparisons are performed.
+#'
+#' @param split.by \code{Character vector} or \code{NULL}. Columns to split by.
+#' Tests are run separately for each combination. (Default: \code{NULL})
+#'
+#' @param pair.by \code{Character scalar} or \code{NULL}. Column for pairing
+#' samples in paired tests. (Default: \code{NULL})
+#'
+#' @param features \code{Character vector} or \code{NULL}. Specific features
+#' to test when using \code{assay.type}. (Default: \code{NULL})
+#'
+#' @param p.adjust.method \code{Character scalar}. Method for p-value
+#' adjustment. (Default: \code{"fdr"})
+#'
+#' @param name \code{Character scalar}. Column name prefix for results.
+#' (Default: \code{"wilcoxon"})
+#'
+#' @param ... Additional arguments passed to \code{rstatix::wilcox_test}.
+#'
+#' @examples
+#' data(GlobalPatterns, package = "mia")
+#' tse <- GlobalPatterns
+#' tse <- tse[1:50, tse$SampleType %in% c("Feces", "Skin")]
+#'
+#' # Test assay values (per feature)
+#' res <- getWilcoxon(tse, assay.type = "counts", formula = ~SampleType)
+#'
+#' # Test colData variable (e.g., alpha diversity)
+#' tse <- mia::addAlpha(tse, index = "shannon_diversity")
+#' res <- getWilcoxon(tse, col.var = "shannon_diversity", formula = ~SampleType)
+#'
+#' @seealso
+#' \code{\link[rstatix:wilcox_test]{rstatix::wilcox_test}},
+#' \code{\link[daa:getTtest]{getTtest}}
+#'
+#' @export
+NULL
+
+#' @rdname getWilcoxon
+#' @export
+#' @importFrom SingleCellExperiment altExp
+#' @importFrom methods callNextMethod
+setMethod("getWilcoxon", "SingleCellExperiment", function (x, ... ){
+    x <- .check_and_get_altExp(x, ...)
+    res <- callNextMethod(x, ...)
+    return(res)
+})
+
+#' @rdname getWilcoxon
+#' @export
+#' @importFrom SummarizedExperiment assay colData rowData
+#' @importFrom rstatix wilcox_test adjust_pvalue
+#' @importFrom S4Vectors DataFrame
+setMethod(
+    "getWilcoxon", "SummarizedExperiment",
+    function (x, assay.type = NULL, row.var = NULL, col.var = NULL,
+             formula, split.by = NULL, pair.by = NULL, features = NULL,
+             p.adjust.method = "fdr", ... ){
+        ############################# Input check ##############################
+        group <- .check_input(
+            x, assay.type, row.var, col.var, formula,
+            split.by, pair.by, features
+        )
+        ########################### Input check end ############################
+        # Get y variable name (the column to test)
+        y <- c(assay.type, row.var, col.var)
+        # Get data based on source
+        df <- .get_data(
+            x, assay.type, row.var, col.var, group,
+            split.by, pair.by, features
+        )
+        # Run tests
+        paired <- !is.null(pair.by)
+        res <- .run_wilcoxon(
+            df, y, group, split.by, paired,
+            p.adjust.method, features, ...
+        )
+        return(res)
+    }
+)
+
+#' @rdname getWilcoxon
+#' @export
+setMethod(
+    "addWilcoxon", "SummarizedExperiment",
+    function (x, name = "wilcoxon", ... ){
+        if( !.is_non_empty_string(name) ){
+            stop("'name' must be a single character value.", call. = FALSE)
+        }
+        res <- getWilcoxon(x, ...)
+        x <- .add_values_to_colData(x, list(res$p.adj), paste0(name, "_padj"),
+            MARGIN = 1
+        )
+        return(x)
+    }
+)
+
+################################################################################
+# Internal function using .calc_daa engine
+################################################################################
+
+#' @importFrom rstatix wilcox_test
+.run_wilcoxon <- function (df, y, group, split.by, paired, p.adjust.method, features = NULL, ... ){
+    .calc_daa(
+        df = df, y = y, group = group, split.by = split.by,
+        paired = paired, FUN = rstatix::wilcox_test,
+        p.adjust.method = p.adjust.method, features = features, ...
+    )
+}