查询给定物种的可用基因组

genomeBuilds()是GenomeInfoDb中的函数，可以列出给定物种的可用基因组。

> genomeBuilds("mouse", style = "UCSC")
  commonName     organism ucscID
1      mouse Mus musculus    mm9
2      mouse Mus musculus   mm10
> genomeBuilds("mouse",style="Ensembl")
  commonName     organism ensemblID
1      mouse Mus musculus   NCBIm37
2      mouse Mus musculus    GRCm38
3      mouse Mus musculus GRCm38.p1
4      mouse Mus musculus GRCm38.p2
5      mouse Mus musculus GRCm38.p3
6      mouse Mus musculus GRCm38.p4
7      mouse Mus musculus GRCm38.p5
8      mouse Mus musculus GRCm38.p6
> genomeBuilds("human", style = "UCSC")
  commonName     organism ucscID
1      human Homo sapiens   hg19
2      human Homo sapiens   hg38
> genomeBuilds("human", style = "Ensembl")
   commonName     organism  ensemblID
1       human Homo sapiens     NCBI36
2       human Homo sapiens     GRCh37
3       human Homo sapiens  GRCh37.p3
4       human Homo sapiens  GRCh37.p5
5       human Homo sapiens  GRCh37.p6
6       human Homo sapiens  GRCh37.p7
7       human Homo sapiens  GRCh37.p8
8       human Homo sapiens GRCh37.p10
9       human Homo sapiens GRCh37.p12
10      human Homo sapiens GRCh37.p11
11      human Homo sapiens GRCh37.p13
12      human Homo sapiens     GRCh38
13      human Homo sapiens  GRCh38.p2
14      human Homo sapiens  GRCh38.p3
15      human Homo sapiens  GRCh38.p5
16      human Homo sapiens  GRCh38.p7
17      human Homo sapiens GRCh38.p10
18      human Homo sapiens GRCh38.p12
19      human Homo sapiens GRCh38.p13

mapGenomeBuilds()可以给出UCSC和Ensembl中基因组的映射关系。

> mapGenomeBuilds("mm10", style = c("UCSC", "Ensembl"))
  commonName     organism ucscID ucscDate ensemblID
1      mouse Mus musculus   mm10 Dec.2011   NCBIm37
2      mouse Mus musculus   mm10 Dec.2011    GRCm38
3      mouse Mus musculus   mm10 Dec.2011 GRCm38.p1
4      mouse Mus musculus   mm10 Dec.2011 GRCm38.p2
5      mouse Mus musculus   mm10 Dec.2011 GRCm38.p3
6      mouse Mus musculus   mm10 Dec.2011 GRCm38.p4
7      mouse Mus musculus   mm10 Dec.2011 GRCm38.p5
8      mouse Mus musculus   mm10 Dec.2011 GRCm38.p6
> mapGenomeBuilds("hg38", style = c("UCSC", "Ensembl"))
  commonName     organism ucscID ucscDate  ensemblID
1      human Homo sapiens   hg38 Dec.2013 GRCh37.p13
2      human Homo sapiens   hg38 Dec.2013     GRCh38
3      human Homo sapiens   hg38 Dec.2013  GRCh38.p2
4      human Homo sapiens   hg38 Dec.2013  GRCh38.p3
5      human Homo sapiens   hg38 Dec.2013  GRCh38.p5
6      human Homo sapiens   hg38 Dec.2013  GRCh38.p7
7      human Homo sapiens   hg38 Dec.2013 GRCh38.p10
8      human Homo sapiens   hg38 Dec.2013 GRCh38.p12
9      human Homo sapiens   hg38 Dec.2013 GRCh38.p13