Dear All,

I want to get genomic coordinates for a list of human genes. I don't quite know where to start and which package(s) to use. Could you guide me which bioconductor packages to use so I can go read those manual by myself. Thanks a lot!

Stephen

The TxDb.Hsapiens.UCSC.hg19.knownGene package is really useful for this task.  You may also need to use the org.Hs.eg.db package to convert from your gene identifiers to/from Entrez Gene IDs.

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
g = genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
head(g)

GRanges object with 6 ranges and 1 metadata column:
            seqnames                 ranges strand |     gene_id
               <Rle>              <IRanges>  <Rle> | <character>
          1    chr19 [ 58858172,  58874214]      - |           1
         10     chr8 [ 18248755,  18258723]      + |          10
        100    chr20 [ 43248163,  43280376]      - |         100
       1000    chr18 [ 25530930,  25757445]      - |        1000
      10000     chr1 [243651535, 244006886]      - |       10000
  100008586     chrX [ 49217763,  49233491]      + |   100008586
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome