fixed: warning after changes in R 4.0.0 as class(emat) is now longer …

…of length 1
peterawe · Jun 11, 2020 · cdb8559 · cdb8559
1 parent 2d7860e
commit cdb8559
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Showing 4 changed files with 5 additions and 6 deletions.
diff --git a/R/ematAdjust.R b/R/ematAdjust.R
@@ -30,6 +30,7 @@
 #' @seealso \code{\link[base]{scale}}, \code{\link[limma]{voom}},
 #' \code{\link[limma]{normalizeBetweenArrays}}
 #' @examples
+#' library(Biobase)
 #' emat <- ematAdjust(crcTCGAsubset[1:100,], normMethod = "quantile")
 #' mean(Biobase::exprs(crcTCGAsubset))    # E[>2]
 #' mean(emat,na.rm=TRUE)             # E[~0]
@@ -40,7 +41,7 @@ ematAdjust <- function(emat, center = TRUE, scale = TRUE, normMethod = NULL,
 
     # checkInput ##############################################################
     if (is.data.frame(emat)) emat <- as.matrix(emat)
-    if (class(emat) == "ExpressionSet") emat <- Biobase::exprs(emat)
+    if (class(emat)[1] == "ExpressionSet") emat <- Biobase::exprs(emat)
     if (!is.null(normMethod)) {
         if (normMethod %in% subData$methods.voom) {
             emat <- limma::normalizeBetweenArrays(log2(emat+.25),

diff --git a/R/ntp.R b/R/ntp.R
@@ -77,7 +77,7 @@ ntp <- function(emat, templates, nPerm = 1000, distance = "cosine",
     # checkInput ##############################################################
 
     # emat tests
-    if (class(emat) == "ExpressionSet")
+    if (class(emat)[1] == "ExpressionSet")
         emat <- suppressPackageStartupMessages(Biobase::exprs(emat))
     if (is.data.frame(emat) | is.vector(emat)) emat <- as.matrix(emat)
     if (is.null(rownames(emat))) stop("missing emat rownames, check input")

diff --git a/R/subCamera.R b/R/subCamera.R
@@ -81,7 +81,7 @@ subCamera <- function(emat, class, keepN = TRUE, batch = NULL,
     # checkInput ##############################################################
 
     fallback.xKey <- NULL
-    if (class(emat) == "ExpressionSet") {
+    if (class(emat)[1] == "ExpressionSet") {
         fallback.xKey <- suppressPackageStartupMessages(Biobase::fData(emat))
         emat <- Biobase::exprs(emat)
     }
@@ -169,8 +169,6 @@ subCamera <- function(emat, class, keepN = TRUE, batch = NULL,
         colnames(design) <- gsub("group", "", colnames(design))
 
         if (doVoom == TRUE) emat <- voomTransform(emat, normMethod, design)
-        fit <- limma::lmFit(emat, design)
-        fit2 <- limma::eBayes(fit)
         mm <- levels(df$group)
 
         # performCamera #######################################################

diff --git a/R/subDEG.R b/R/subDEG.R
@@ -47,7 +47,7 @@ subDEG <- function(emat, class, batch=NULL, keepN=TRUE, doPairwise = FALSE,
     #  test/fix/clean input
     ###########################################################################
 
-    if (class(emat) == "ExpressionSet") {
+    if (class(emat)[1] == "ExpressionSet") {
         if (is.null(feat)) feat <- Biobase::fData(emat)
         emat <- Biobase::exprs(emat)
     }