Seeks good way to convert GB_LIST to SYMBOL
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4.3 years ago
MatthewP ★ 1.4k

Take GPL5188 as example. This GPL map probe id to GB_LIST(genebank).

> gpl <- getGEO("GPL5188", AnnotGPL=FALSE, destdir=".")
> as_tibble(Table(gpl)) %>% dplyr::select(ID, GB_LIST) %>% head(n = 3)
# A tibble: 3 x 2
       ID GB_LIST                     
    <dbl> <chr>                       
1 2315101 NR_024005,NR_024004,AK093685
2 2315102 NR_024004,NR_024005,AK093685
3 2315103 ""

I want to map probe id to SYMBOL, so I use ACCNUM and SYMBOL field in org.Hs.eg.db.

> gblist <- c("NR_024004", "AK093685", "NR_024005", "AB007962", "BC063535")
> gbMap <- AnnotationDbi::select(org.Hs.eg.db, keys=gblist, keytype="ACCNUM", columns=c("ACCNUM", "SYMBOL"))
'select()' returned 1:1 mapping between keys and columns
> head(gbMap)
     ACCNUM    SYMBOL
1 NR_024004   DDX11L2
2  AK093685   DDX11L2
3 NR_024005   DDX11L2
4  AB007962 LINC00869
5  BC063535 LINC00623

This GPL5188 has multiple id in GB_LIST separate by ",", I only take the first one to map to symbol. But I lost most of my probe after doing that. Maybe some symbol are actually map to 2/3 one in GB_LIST. Any other way to convert such GB_LIST to SYMBOL? Thanks.

geo • 2.2k views
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