you're a little behind on BSgenome version, but consider values(tdata)$tx_id
etc., which may be the way to do what you want On Tue, Mar 2, 2010 at 4:52 PM, joseph <[email protected]> wrote: > Hello > > I tried to reproduce the analysis in GenomicFeatures vignette section 2.7.2 > (Example: Retrieving data from an RNA-seq experiment); > I got the error below. Can you please help me? > Thanks > > >> txdb <- loadFeatures(system.file("extdata", "UCSC_knownGene_sample.sqlite", >> package="GenomicFeatures")) >> gr <- GRanges(seqnames = rep("chr5",4), ranges = IRanges(start = >> c(244620,244670,245804,247502), end = c(244652,244702,245836,247534)), >> strand = rep("+",4)) >> annotGR <- transcriptsByRanges(txdb, gr, columns=c("tx_id", "tx_name", >> "gene_id", "exon_id")) >> OL <- findOverlaps(gr, annotGR, multiple=TRUE) >> tdata <- annotGR[subjectHits(OL),] > >> table(tdata$tx_id) > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges >> table(unlist(tdata$gene_id)) > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges > Error in unlist(tdata$gene_id) : > error in evaluating the argument 'x' in selecting a method for function > 'unlist' >> > >> sessionInfo() > R version 2.11.0 Under development (unstable) (2010-02-21 r51163) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures.Mmusculus.UCSC.mm9_0.1.1 > [2] GenomicFeatures_0.3.38 > [3] ShortRead_1.5.18 > [4] lattice_0.18-3 > [5] BSgenome_1.15.10 > [6] Biostrings_2.15.22 > [7] IRanges_1.5.49 > [8] rtracklayer_1.7.10 > [9] RCurl_1.3-1 > [10] bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.7.4 biomaRt_2.3.4 DBI_0.2-5 grid_2.11.0 hwriter_1.1 > [6] RSQLite_0.8-3 tools_2.11.0 XML_2.6-0 >> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
