bioc check

PYangLab · Jun 24, 2024 · 9366bcd · 9366bcd
1 parent bfb2de7
commit 9366bcd
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Showing 4 changed files with 29 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,7 +35,8 @@ Imports:
     reshape2,
     BiocParallel,
     stats,
-    dplyr
+    dplyr,
+    purrr
 biocViews: Classification, GeneExpression, SingleCell, Software, Sequencing, DifferentialExpression
 Suggests: 
     knitr,

diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Cepo authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Cepo authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/R/Cepo.R b/R/Cepo.R
@@ -6,7 +6,7 @@
 #' Default to NULL to not remove any genes.
 #' @param prefilter_sd Numeric value indicating threshold relating to standard 
 #' deviation of genes. Used with prefilter_zeros. 
-#' @param prefilter_pzeros Numeric value indicating threshold relating to the 
+#' @param prefilter_pzero Numeric value indicating threshold relating to the 
 #' percentage of zero expression of genes. Used with prefilter_sd. 
 #' @param logfc Numeric value indicating the threshold of log fold-change 
 #' to use to filter genes.
@@ -39,6 +39,7 @@
 #' @importFrom HDF5Array HDF5Array
 #' @importFrom BiocParallel SerialParam MulticoreParam SnowParam bplapply
 #' @importFrom stats pnorm pchisq
+#' @importFrom purrr map map2
 #' @import dplyr
 #' @return Returns a list of key genes.
 #' @description ExprsMat accepts various matrix objects, 
@@ -258,8 +259,8 @@ bootFastCepo <- function(exprsMat, cellTypes, minCells, exprsPct, logfc, variabi
             this_celltype_stats_matrix = purrr::map(.x = sampled_cepo_stats, .f = function(this_sampled_stats){
                 this_sampled_stats[,this_celltype]
             }) %>% do.call(cbind, .)
-            this_celltype_stats_mean = Cepo:::rowMeans_withnames(this_celltype_stats_matrix)
-            this_celltype_stats_sd = Cepo:::rowSds_withnames(this_celltype_stats_matrix)
+            this_celltype_stats_mean = rowMeans_withnames(this_celltype_stats_matrix)
+            this_celltype_stats_sd = rowSds_withnames(this_celltype_stats_matrix)
             return(data.frame(mean = this_celltype_stats_mean, sd = this_celltype_stats_sd))
         })
     names(celltype_norm_stats) = cts