Converting between UCSC id and gene symbol with bioconductor annotation resources
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kstachelek • 0
Last seen 16 months ago
United States

I would like to convert between what I think are UCSC transcript ids and gene symbols (see example below).

What is the correct name for this identifier? I found the key TXNAME in txdb. Is there a corresponding key in orgdb? How can I get a description of the keys in an annotation resource? Or can I head an annotation resource to see examples of keys?

example: uc010whp.2 -> BRCA1

AnnotationData AnnotationDbi annotation • 1.4k views
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Last seen 1 day ago
United States

You need to use the Homo.sapiens package to make that mapping.

> library(Homo.sapiens)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    anyDuplicated, append,, basename, cbind, colnames,
    dirname,, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax,, pmin,, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    expand.grid, I, unname

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':


Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package:

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
> select(Homo.sapiens, "uc010whp.2", "SYMBOL","TXNAME")
'select()' returned 1:1 mapping between keys and columns
1 uc010whp.2  BRCA1

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