@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read

         methods to work with GMAP and GSNAP from within R. In addition,

         it provides methods to tally alignment results on a

         per-nucleotide basis using the bam_tally tool.

-Version: 1.13.10

+Version: 1.13.11

 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),

         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)

 Imports: S4Vectors (>= 0.9.25), IRanges, 

@@ -39,7 +39,7 @@ exonsToGene <- range

 getExons <- function(txdb, orgdb, gene) {

   eg <- AnnotationDbi::select(orgdb, gene, "ENTREZID", "SYMBOL")$ENTREZID

-  exons(txdb, vals = list(gene_id=eg))

+  exons(txdb, filter = list(gene_id=eg))

 }

 getGeneRoi <- function(txdb, orgdb, gene, extend=1e6) {

@@ -165,7 +165,7 @@ library("org.Hs.eg.db")

 library("TxDb.Hsapiens.UCSC.hg19.knownGene")

 eg <- org.Hs.eg.db::org.Hs.egSYMBOL2EG[["TP53"]]

 txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

-tx <- transcripts(txdb, vals = list(gene_id = eg))

+tx <- transcripts(txdb, filter = list(gene_id = eg))

 roi <- range(tx) + 1e6

 strand(roi) <- "*"

 @