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
>
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