seqinfo()基本操作

seqinfo()是GenomeInfoDb程序的一个函数，用于获取基因组序列的基本信息，这个函数在运行时需要调用fetchExtendedChromInfoFromUCSC()，因此，需要保持网络连接。基本用法是

Seqinfo(genome="")

以获取hg38的基因组信息为例

> x <- Seqinfo(genome="hg38")
> x
Seqinfo object with 455 sequences (1 circular) from hg38 genome:
  seqnames         seqlengths isCircular genome
  chr1              248956422      FALSE   hg38
  chr2              242193529      FALSE   hg38
  chr3              198295559      FALSE   hg38
  chr4              190214555      FALSE   hg38
  chr5              181538259      FALSE   hg38
  ...                     ...        ...    ...
  chrUn_KI270753v1      62944      FALSE   hg38
  chrUn_KI270754v1      40191      FALSE   hg38
  chrUn_KI270755v1      36723      FALSE   hg38
  chrUn_KI270756v1      79590      FALSE   hg38
  chrUn_KI270757v1      71251      FALSE   hg38

> summary(x)
[1] "455 sequences (1 circular) from hg38 genome"

> length(x)
[1] 455

另外，还有如下Accessors可以调用

seqnames(x)
names(x)
seqlevels(x)
seqlengths(x)
isCircular(x)
genome(x)

比如：

> head(seqnames(x))
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6"
> head(names(x))
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6"
> head(seqlevels(x))
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6"
> head(seqlengths(x))
     chr1      chr2      chr3      chr4      chr5      chr6 
248956422 242193529 198295559 190214555 181538259 170805979 
> head(isCircular(x))
 chr1  chr2  chr3  chr4  chr5  chr6 
FALSE FALSE FALSE FALSE FALSE FALSE 
> head(genome(x))
  chr1   chr2   chr3   chr4   chr5   chr6 
"hg38" "hg38" "hg38" "hg38" "hg38" "hg38"

也可以直接抽取其中的序列，比如：

> x[c("chrY", "chr3", "chr1")]
Seqinfo object with 3 sequences from hg38 genome:
  seqnames seqlengths isCircular genome
  chrY       57227415      FALSE   hg38
  chr3      198295559      FALSE   hg38
  chr1      248956422      FALSE   hg38

或者，甚至可以自己定义：

> y <- Seqinfo(seqnames=c("chr1", "chr2", "chr3", "chrM"),
             seqlengths=c(100, 200, NA, 15),
             isCircular=c(NA, FALSE, FALSE, TRUE),
             genome="toy")
> y
Seqinfo object with 4 sequences (1 circular) from toy genome:
  seqnames seqlengths isCircular genome
  chr1            100         NA    toy
  chr2            200      FALSE    toy
  chr3             NA      FALSE    toy
  chrM             15       TRUE    toy