Merge branch 'master' of github.com:stemangiola/tidybulk

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidybulk
 Title: Brings transcriptomics to the tidyverse 
-Version: 1.17.3
+Version: 1.17.8
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -95,7 +95,7 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/tidybulk
 BugReports: https://github.com/stemangiola/tidybulk/issues

NAMESPACE

@@ -87,6 +87,7 @@ importFrom(GenomicRanges,makeGRangesListFromDataFrame)
 importFrom(Matrix,colSums)
 importFrom(S4Vectors,metadata)
 importFrom(SummarizedExperiment,SummarizedExperiment)
+importFrom(SummarizedExperiment,as.data.frame)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)

R/cibersort.R

@@ -255,12 +255,9 @@ my_CIBERSORT <- function(Y, X, perm=0, QN=TRUE, cores = 3, exp_transform = FALSE
     ))
   Y=Y[,colSums(Y)>0, drop=FALSE]
 
-  # Check if package is installed, otherwise install
-  if (find.package("matrixStats", quiet = TRUE) %>% length %>% equals(0)) {
-    message("tidybulk says: Installing matrixStats needed for cibersort")
-    install.packages("matrixStats", repos = "https://cloud.r-project.org")
-  }
-
+  # Check if 'matrixStats' package is installed, otherwise stop with instructions
+  check_and_install_packages("matrixStats")
+
   # Eliminate sd == 0
   if(length(which(matrixStats::colSds(Y)==0))>0)
     warning(sprintf(