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Factors in tx2gene cause issues #12

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2 changes: 2 additions & 0 deletions R/constructors.R
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Expand Up @@ -71,6 +71,8 @@ stageRTx <- function(pScreen, pConfirmation, pScreenAdjusted=FALSE, tx2gene){
stop("not all transcript names in pConfirmation match with a transcript ID from the tx2gene object.")
if(any(is.na(match(names(pScreen),tx2gene[,2]))))
stop("not all gene names in pScreen match with a gene ID from the tx2gene object.")
if(class(tx2gene[,1]) == "factor" | class(tx2gene[,2]) == "factor")
stop("columns of tx2gene should be character, not factor")
stageR <- new("stageRTx")
stageR@pScreen <- pScreen
stageR@pConfirmation <- pConfirmation
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