del slow functions

noriakis · Apr 28, 2024 · acc6727 · acc6727
1 parent e1c6948
commit acc6727
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Showing 7 changed files with 397 additions and 518 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -21,9 +21,7 @@ export(compareGenes)
 export(consensusSeq)
 export(consensusSeqGeneral)
 export(consensusSeqMIDAS1)
-export(consensusSeqMIDAS1Slow)
 export(consensusSeqMIDAS2)
-export(consensusSeqMIDAS2Slow)
 export(convertWideToMaf)
 export(doAdonis)
 export(doBoruta)

diff --git a/R/compareGenes.R b/R/compareGenes.R
@@ -31,7 +31,7 @@ compareGenes <- function(stana, species=NULL, geneID=NULL, cl=NULL, argList=list
 	}
 	if (length(names(cl))!=2) {stop("Only two grouping is allowed")}
 	resList <- list()
-	qqcat("Testing total of @{nrow(geneDf)}\n")
+	cat_subtle("# Testing total of ", nrow(geneDf), "\n", sep="")
 	for (i in row.names(geneDf)) {
 		x <- geneDf[i, intersect(colnames(geneDf), cl[[1]])] |> as.numeric()
 		y <- geneDf[i, intersect(colnames(geneDf), cl[[2]])] |> as.numeric()