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Yuan Jian
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250
@yuan-jian-2603
Last seen 8.8 years ago
hello,
I can access hg19 but not hg18 using makeTranscriptDbFromUCSC. can
anyone tell me how to access hg18?
>library(GenomicFeatures)
> hg18KG <- makeTranscriptDbFromUCSC(genome = "hg18", tablename =
"knownGene")
Download the knownGene table ... Error in curlPerform(url = url,
headerfunction = header$update, curl = curl, :
transfer closed with outstanding read data remaining
> hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
"knownGene")
Download the knownGene table ... OK
Download the knownToLocusLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.0.6 GenomicRanges_1.0.1 IRanges_1.6.8
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 biomaRt_2.4.0 Biostrings_2.16.9
BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-2
[7] RSQLite_0.9-1 rtracklayer_1.8.1 tools_2.11.1 XML_3.1-0
>
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