PrepareAnnotationRefseq2 function error!
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yeh234 • 0
@yeh234-11300
Last seen 6.3 years ago
Hello everyone,

I follow the "customProDB"  tutorial for prepare annotation files and use "PGA package"  PrepareAnnotationRefseq2 function. But I got an error message and fail to generate depentent RData.

Am I current run R input below,

> options(width=70)
> transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499", "NM_004448",
+ "NM_000179", "NR_029605", "NM_004333", "NM_001127511")
> pepfasta <- system.file("extdata", "refseq_pro_seq.fasta",
+ package="customProDB")
> CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta",
+ package="customProDB")
> annotation_path <- tempdir()
> PrepareAnnotationRefseq2(genome='hg19', CDSfasta, pepfasta, annotation_path,
+ dbsnp = NULL, transcript_ids=transcript_ids,
+ splice_matrix=FALSE, COSMIC=FALSE)
Build TranscriptDB object (txdb.sqlite) ... 
Download the refGene table ... OK
Download the hgFixed.refLink 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 TxDb object ... OK
 done
Prepare gene/transcript/protein id mapping information (ids.RData) ... Error in normArgTable(value, x) : unknown table name 'refLink'

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

PGA_1.2.2; customProDB_1.12.0    


> traceback()
9: stop("unknown table name '", name, "'")
8: normArgTable(value, x)
7: .local(x, ..., value)
6: `tableName<-`(`*tmp*`, value = "refLink")
5: `tableName<-`(`*tmp*`, value = "refLink")
4: .local(x, ...)
3: ucscTableQuery(session, "refGene", table = "refLink", names = refGene[, 
       "name2"])
2: ucscTableQuery(session, "refGene", table = "refLink", names = refGene[, 
       "name2"])
1: PrepareAnnotationRefseq2(genome = "hg19", CDSfasta, pepfasta, 
       annotation_path, dbsnp = NULL, transcript_ids = transcript_ids, 
       splice_matrix = FALSE, COSMIC = FALSE)
 


Does anyone can help me to solve this error.

 

Thank you,

mbird

PGA customprodb • 817 views
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