Include package.R file to avoid undefined function.

DavisLaboratory · Mar 26, 2024 · 03dc19f · 03dc19f
1 parent e6ba036
commit 03dc19f
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,10 +20,10 @@ Collate:
     'tf_idf_iae_wrappers.R'
     'score.R'
     'AllGenerics.R'
+    'smartid-package.R'
     'gs_score-methods.R'
     'plot.R'
     'scale_mgm.R'
-    'smartid-package.R'
     'score-methods.R'
     'select_markers.R'
     'top_markers.R'

diff --git a/R/gs_score-methods.R b/R/gs_score-methods.R
@@ -1,4 +1,4 @@
-#' @include score.R
+#' @include score.R smartid-package.R
 NULL
 
 #' @rdname gs_score

diff --git a/R/score-methods.R b/R/score-methods.R
@@ -42,10 +42,10 @@ setMethod(
     expr <- SummarizedExperiment::assay(data, i = slot)
     ## get label
     if (!is.null(par.idf) & !is.null(par.idf$label)) {
-      par.idf$label <- colData(data)[[par.idf$label]]
+      par.idf$label <- SummarizedExperiment::colData(data)[[par.idf$label]]
     }
     if (!is.null(par.iae) & !is.null(par.iae$label)) {
-      par.iae$label <- colData(data)[[par.iae$label]]
+      par.iae$label <- SummarizedExperiment::colData(data)[[par.iae$label]]
     }
 
     res <- cal_score(

diff --git a/R/top_markers-methods.R b/R/top_markers-methods.R
@@ -1,4 +1,4 @@
-#' @include top_markers.R
+#' @include top_markers.R smartid-package.R
 NULL
 
 #' @rdname top_markers
@@ -63,7 +63,7 @@ setMethod(
     ## get expr
     expr <- SummarizedExperiment::assay(data, i = slot)
     ## get label
-    label <- colData(data)[[label]]
+    label <- SummarizedExperiment::colData(data)[[label]]
 
     top_m <- top_markers(
       data = expr,