AnnBuilder package: problem with basefile type of
0
0
Entering edit mode
Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.3 years ago
Hi, Weijun, Thanks for the information. It is a bug. The code uses "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz" for refseq to Entrez Gene mapping. It should use "gene2refseq.gz" instead. The bug has been fixed and version number increased to 1.11.5. The update is available on svn now, and will be available on web at around 1pm, July 26 (Pacific Time). If you are in a hurry, this is the modification: ================================================== --- ABPkgBuilder.R (v1.11.4) +++ ABPkgBuilder.R (v1.11.5) @@ -558,11 +557,12 @@ } getUniMappings <- function(baseName, eg, ug, otherSrc, baseMapType){ - base <- getBaseFile(baseName) if(baseMapType == "refseq"){ - unified <- unifyMappings(base, eg, NULL, otherSrc) + eg_refseq <- eg + eg_refseq at accession <- eg_refseq at refseq + unified <- unifyMappings(base, eg_refseq, NULL, otherSrc) }else if(baseMapType != "ll"){ #ug <- UG(srcUrl = srcUrl(ug), # parser = parser(ug), baseFile = baseName(ug), =================================================== Also, notice that the ACCNUM environment generated by AnnBuilder is a copy of your input, not probe-to-GenBank mapping. ABPkgBuilder doesn't provide probe-to-GenBank mapping unless baseFile contains that information. hope it works this time :P nianhua
AnnBuilder AnnBuilder • 458 views
ADD COMMENT

Login before adding your answer.

Traffic: 277 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6