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adjustments in response to the vals -> filter renaming in GenomicFeatures

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@115831 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 05/04/2016 22:55:27
Showing3 changed files

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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.13.10
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+Version: 1.13.11
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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 Imports: S4Vectors (>= 0.9.25), IRanges, 
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@@ -39,7 +39,7 @@ exonsToGene <- range
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 getExons <- function(txdb, orgdb, gene) {
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   eg <- AnnotationDbi::select(orgdb, gene, "ENTREZID", "SYMBOL")$ENTREZID
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-  exons(txdb, vals = list(gene_id=eg))
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+  exons(txdb, filter = list(gene_id=eg))
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 }
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 getGeneRoi <- function(txdb, orgdb, gene, extend=1e6) {
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@@ -165,7 +165,7 @@ library("org.Hs.eg.db")
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 library("TxDb.Hsapiens.UCSC.hg19.knownGene")
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 eg <- org.Hs.eg.db::org.Hs.egSYMBOL2EG[["TP53"]]
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 txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
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-tx <- transcripts(txdb, vals = list(gene_id = eg))
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+tx <- transcripts(txdb, filter = list(gene_id = eg))
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 roi <- range(tx) + 1e6
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 strand(roi) <- "*"
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 @