correct a few class == tests

RGLab · Nov 30, 2022 · 339c6a7 · 339c6a7
1 parent 16e90b4
commit 339c6a7
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/R/Fluidigm-methods.R b/R/Fluidigm-methods.R
@@ -118,7 +118,7 @@ getConcordance <- function(singleCellRef, singleCellcomp, groups=NULL, fun.natur
         m <- as(scL[[i]], 'data.table')
         tmp <- reshape2::dcast(m, firstForm, fun.aggregate=fun.natural)
         ##exponential average per gene, scaled by number of cells
-        if(class(m[['ncells']]) == 'factor'){
+        if(inherits(m[['ncells']], 'factor')){
             warning("ncells is a factor rather than numeric.\n I'll continue, but this may cause problems down the line")
             tmp[['ncells']] <- as.numeric(as.character(tmp[["ncells"]]))
         }

diff --git a/R/Hypothesis.R b/R/Hypothesis.R
@@ -36,7 +36,7 @@ Hypothesis <- CoefficientHypothesis <- function(hypothesis, terms){
 generateHypothesis <- function(h, terms){
     stopifnot(inherits(h, 'Hypothesis') | inherits(h, 'CoefficientHypothesis'))
     ## if(length(h@transformed)>0) return(h)
-    if(class(h) =='Hypothesis'){
+    if(class(h) =='Hypothesis'){ #we need to test for this exact class, not just inheritance
         ## makeContrasts can't handle non-syntactic names :-/
         ## So we'll use this instead
         cm <- makeContrasts2(contrasts=h@.Data, levels=terms)

diff --git a/R/Readers.R b/R/Readers.R
@@ -197,7 +197,7 @@ if(getRversion() >= "2.15.1") globalVariables(c('Ct Call', 'Ct Value', 'Gene'))
 ##Function to read fluidigm from xls file
 read.fluidigm.xls<-function(x,header.size=2,skip=8){
     colmap<-c(`Chamber ID`="Chamber.ID",`Sample Name`="SampleName",`Sample Type`="SampleType",`Sample rConc`="SampleRConc",`FAM-MGB Name`="Gene",`FAM-MGB Type`="AssayType",`Ct Quality`="CtQuality",`Ct Threshold`="CtThreshold")
-    if(!class(x)=="character"){
+    if(!inherits(x, "character")){
         message("Argument must be of type character")
     }
     if(!file.exists(x)){