From 7bc806cb229cea11cfb1ef88653d314fc160d401 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jordi=20Estell=C3=A9?= Date: Fri, 23 Aug 2019 16:09:51 +0200 Subject: [PATCH] Update phyloseq_to_metagenomeSeq function This function crashes on line 50 as follows: > data.frame(tax_table(physeq)) Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent The proposed change is to use instead: > data.frame(tax_table(physeq)@.Data) --- R/extend_metagenomeSeq.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/extend_metagenomeSeq.R b/R/extend_metagenomeSeq.R index 766a07d7..42046a98 100644 --- a/R/extend_metagenomeSeq.R +++ b/R/extend_metagenomeSeq.R @@ -47,7 +47,7 @@ phyloseq_to_metagenomeSeq = function(physeq, ...){ # Create taxa annotation if possible if(!is.null(tax_table(physeq,FALSE))){ TDF = AnnotatedDataFrame(data.frame(OTUname = taxa_names(physeq), - data.frame(tax_table(physeq)),row.names = taxa_names(physeq))) + data.frame(tax_table(physeq)@.Data),row.names = taxa_names(physeq))) } else { TDF = AnnotatedDataFrame(data.frame(OTUname = taxa_names(physeq), row.names = taxa_names(physeq)))