@@ -1,25 +1,31 @@

 #' @title Obtain the gene module of a gene of interest

 #' @description This function will output the corresponding feature module for

 #'  a specified vector of genes from a celda_CG or celda_G \code{celdaModel}.

-#'  \code{feature} must match the rownames of \code{sce}.

+#'  \code{features} must match the rownames of \code{sce}.

 #' @param sce A \linkS4class{SingleCellExperiment} object returned by

 #'  \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

-#' @param feature Character vector. Identify feature modules for the specified

+#' @param features Character vector. Identify feature modules for the specified

 #'  feature names. \code{feature} must match the rownames of \code{sce}.

 #' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param exactMatch Logical. Whether to look for exactMatch of the gene name

 #'  within counts matrix. Default \code{TRUE}.

-#' @return List. Each entry corresponds to the feature module determined for

-#' the provided features.

+#' @param by Character. Where to search for \code{features} in the sce object.

+#' If set to \code{"rownames"} then the features will be searched for among

+#' rownames(sce). This can also be set to one of the \code{colnames} of

+#' rowData(sce). Default \code{"rownames"}.

+#' @return Numeric vector containing the module numbers for each feature. If

+#' the feature was not found, then an \code{NA} value will be returned in that

+#' position. If no features were found, then an error will be given.

 #' @export

 setGeneric("featureModuleLookup",

     function(sce,

-        feature,

+        features,

         altExpName = "featureSubset",

-        exactMatch = TRUE) {

+        exactMatch = TRUE,

+        by = "rownames") {

         standardGeneric("featureModuleLookup")})

@@ -27,57 +33,32 @@ setGeneric("featureModuleLookup",

 #' @examples

 #' data(sceCeldaCG)

 #' module <- featureModuleLookup(sce = sceCeldaCG,

-#'     feature = c("Gene_1", "Gene_XXX"))

+#'     features = c("Gene_1", "Gene_XXX"))

 #' @export

 #' @rdname featureModuleLookup

 setMethod("featureModuleLookup", signature(sce = "SingleCellExperiment"),

     function(sce,

-        feature,

+        features,

         altExpName = "featureSubset",

-        exactMatch = TRUE) {

+        exactMatch = TRUE,

+        by = "rownames") {

-        altExp <- SingleCellExperiment::altExp(sce, altExpName)

+        modules <- as.numeric(celdaModules(sce, altExpName = altExpName))

+        

         if (celdaModel(sce, altExpName = altExpName) %in%

                 c("celda_CG", "celda_G")) {

-            featureList <- .featureModuleLookup(sce = altExp,

-                feature = feature,

-                exactMatch = exactMatch)

+          altExp <- SingleCellExperiment::altExp(sce, altExpName)

+          featureIndex <- retrieveFeatureIndex(features, x = altExp,

+                exactMatch = exactMatch, by = by)

+          featureModules <- modules[featureIndex]

+          names(featureModules) <- features  

         } else {

             stop("S4Vectors::metadata(altExp(sce, altExpName))$",

                 "celda_parameters$model must be",

                 " one of 'celda_G', or 'celda_CG'")

         }

-        return(featureList)

+        return(featureModules)

     }

 )

-.featureModuleLookup <- function(sce, feature, exactMatch) {

-    if (!isTRUE(exactMatch)) {

-        feature <- unlist(lapply(

-            seq(length(feature)),

-            function(x) {

-                rownames(sce)[grep(feature[x], rownames(sce))]

-            }

-        ))

-    }

-

-    featList <- lapply(

-        seq(length(feature)),

-        function(x) {

-            if (feature[x] %in% rownames(sce)) {

-                return(SummarizedExperiment::rowData(

-                    sce)$celda_feature_module[which(rownames(sce) ==

-                        feature[x])])

-            } else {

-                return(paste0(

-                    "No feature was identified matching '",

-                    feature[x],

-                    "'."

-                ))

-            }

-        }

-    )

-    names(featList) <- feature

-    return(featList)

-}

@@ -7,16 +7,18 @@

 \usage{

 featureModuleLookup(

   sce,

-  feature,

+  features,

   altExpName = "featureSubset",

-  exactMatch = TRUE

+  exactMatch = TRUE,

+  by = "rownames"

 )

 \S4method{featureModuleLookup}{SingleCellExperiment}(

   sce,

-  feature,

+  features,

   altExpName = "featureSubset",

-  exactMatch = TRUE

+  exactMatch = TRUE,

+  by = "rownames"

 )

 }

 \arguments{

@@ -25,7 +27,7 @@ featureModuleLookup(

 located in the \code{useAssay} assay slot.

 Rows represent features and columns represent cells.}

-\item{feature}{Character vector. Identify feature modules for the specified

+\item{features}{Character vector. Identify feature modules for the specified

 feature names. \code{feature} must match the rownames of \code{sce}.}

 \item{altExpName}{The name for the \link{altExp} slot

@@ -33,18 +35,24 @@ to use. Default "featureSubset".}

 \item{exactMatch}{Logical. Whether to look for exactMatch of the gene name

 within counts matrix. Default \code{TRUE}.}

+

+\item{by}{Character. Where to search for \code{features} in the sce object.

+If set to \code{"rownames"} then the features will be searched for among

+rownames(sce). This can also be set to one of the \code{colnames} of

+rowData(sce). Default \code{"rownames"}.}

 }

 \value{

-List. Each entry corresponds to the feature module determined for

-the provided features.

+Numeric vector containing the module numbers for each feature. If

+the feature was not found, then an \code{NA} value will be returned in that

+position. If no features were found, then an error will be given.

 }

 \description{

 This function will output the corresponding feature module for

  a specified vector of genes from a celda_CG or celda_G \code{celdaModel}.

- \code{feature} must match the rownames of \code{sce}.

+ \code{features} must match the rownames of \code{sce}.

 }

 \examples{

 data(sceCeldaCG)

 module <- featureModuleLookup(sce = sceCeldaCG,

-    feature = c("Gene_1", "Gene_XXX"))

+    features = c("Gene_1", "Gene_XXX"))

 }

@@ -182,11 +182,7 @@ test_that(desc = "Testing featureModuleLookup with celda_CG", {

     res <- featureModuleLookup(modelCG, "Gene_1")

     expect_true(res == celdaModules(modelCG)[1])

-    res <- featureModuleLookup(modelCG, "Gene_2", exactMatch = FALSE)

-    expect_true(length(res) == 11)

-

-    res <- featureModuleLookup(modelCG, "XXXXXXX")

-    expect_true(grepl("No feature", res))

+    expect_error(featureModuleLookup(modelCG, "XXXXXXX"))

 })