error in makeTranscriptDbFromUCSC of library(GenomicFeatures)
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Yuan Jian ▴ 250
@yuan-jian-2603
Last seen 8.2 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 > [[alternative HTML version deleted]]
TranscriptDb TranscriptDb • 834 views
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