From d439177f084d3866e37c3c852b0f151372c24619 Mon Sep 17 00:00:00 2001 From: mschubertv Date: Mon, 6 Nov 2023 10:57:44 +0000 Subject: [PATCH] allow 'ANY' txdb, eg. EnsDb objects --- R/methods-predictCoding.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/methods-predictCoding.R b/R/methods-predictCoding.R index f9bba8e..bf2e455 100644 --- a/R/methods-predictCoding.R +++ b/R/methods-predictCoding.R @@ -2,14 +2,14 @@ ### predictCoding methods ### ========================================================================= -setMethod("predictCoding", c("IntegerRanges", "TxDb", "ANY", "DNAStringSet"), +setMethod("predictCoding", c("IntegerRanges", "ANY", "ANY", "DNAStringSet"), function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE) { callGeneric(as(query, "GRanges"), subject, seqSource, varAllele, ..., ignore.strand=ignore.strand) }) -setMethod("predictCoding", c("CollapsedVCF", "TxDb", "ANY", "missing"), +setMethod("predictCoding", c("CollapsedVCF", "ANY", "ANY", "missing"), function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE) { rd <- rowRanges(query) @@ -29,7 +29,7 @@ setMethod("predictCoding", c("CollapsedVCF", "TxDb", "ANY", "missing"), res }) -setMethod("predictCoding", c("ExpandedVCF", "TxDb", "ANY", "missing"), +setMethod("predictCoding", c("ExpandedVCF", "ANY", "ANY", "missing"), function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE) { if (is(alt(query), "CharacterList")) { @@ -39,14 +39,14 @@ setMethod("predictCoding", c("ExpandedVCF", "TxDb", "ANY", "missing"), ignore.strand=ignore.strand) }) -setMethod("predictCoding", c("GRanges", "TxDb", "ANY", "DNAStringSet"), +setMethod("predictCoding", c("GRanges", "ANY", "ANY", "DNAStringSet"), function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE) { .predictCoding(query, subject, seqSource, varAllele, ..., ignore.strand=ignore.strand) }) -setMethod("predictCoding", c("VRanges", "TxDb", "ANY", "missing"), +setMethod("predictCoding", c("VRanges", "ANY", "ANY", "missing"), function(query, subject, seqSource, varAllele, ..., ignore.strand=FALSE) { varAllele <- alt(query)