==========================
dim(t1)
attributes(t1) #综合输出所有行名、列名、以及class结果。
str(t1) #显示每个变量的行列数和类型
class(t1) #查看变量类型，vector、data.frame、matrix、factor、list
mode(t1) #查看数据大类，character、numeric、logical
typeof(t1) #查看数据细类，integer、double、single、float
==========================
> dim(t1) #
NULL
>
> attributes(t1) #综合输出所有行名、列名、以及class结果。
$seqnames
factor-Rle of length 410519 with 30 runs
Lengths: 25139 ... 9
Values : chr1 ... chrUn_JH584304
Levels(66): chr1 chr2 ... chrUn_GL456396 chrUn_JH584304
$strand
factor-Rle of length 410519 with 48 runs
Lengths: 12327 12812 16807 ... 8 19
Values : + - + ... + -
Levels(3): + - *
$ranges
IRanges object with 410519 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 4807788 4807982 195
[2] 4807823 4807982 160
[3] 4807830 4807982 153
[4] 4807892 4807982 91
[5] 4807896 4807982 87
... ... ... ...
[410515] 55112 55701 590
[410516] 56986 57151 166
[410517] 58564 58835 272
[410518] 58564 59690 1127
[410519] 59592 59667 76
$seqinfo
Seqinfo object with 66 sequences (1 circular) from mm10 genome:
seqnames seqlengths isCircular genome
chr1 195471971 <NA> mm10
chr2 182113224 <NA> mm10
chr3 160039680 <NA> mm10
chr4 156508116 <NA> mm10
chr5 151834684 <NA> mm10
... ... ... ...
chrUn_GL456392 23629 <NA> mm10
chrUn_GL456393 55711 <NA> mm10
chrUn_GL456394 24323 <NA> mm10
chrUn_GL456396 21240 <NA> mm10
chrUn_JH584304 114452 <NA> mm10
$elementMetadata
DataFrame with 410519 rows and 2 columns
exon_id geneid
<integer> <character>
1 18 18777
2 19 18777
3 20 18777
4 21 18777
5 22 18777
... ... ...
410515 447554 66776
410516 447555 66776
410517 447556 66776
410518 447557 66776
410519 447558 66776
$elementType
[1] "ANY"
$metadata
$metadata$genomeInfo
$metadata$genomeInfo$`Db type`
[1] "TxDb"
$metadata$genomeInfo$`Supporting package`
[1] "GenomicFeatures"
$metadata$genomeInfo$`Data source`
[1] "UCSC"
$metadata$genomeInfo$Genome
[1] "mm10"
$metadata$genomeInfo$Organism
[1] "Mus musculus"
$metadata$genomeInfo$`Taxonomy ID`
[1] "10090"
$metadata$genomeInfo$`UCSC Table`
[1] "knownGene"
$metadata$genomeInfo$`UCSC Track`
[1] "GENCODE VM23"
$metadata$genomeInfo$`Resource URL`
[1] "http://genome.ucsc.edu/"
$metadata$genomeInfo$`Type of Gene ID`
[1] "Entrez Gene ID"
$metadata$genomeInfo$`Full dataset`
[1] "yes"
$metadata$genomeInfo$`miRBase build ID`
[1] NA
$metadata$genomeInfo$transcript_nrow
[1] "142446"
$metadata$genomeInfo$exon_nrow
[1] "447558"
$metadata$genomeInfo$cds_nrow
[1] "243727"
$metadata$genomeInfo$`Db created by`
[1] "GenomicFeatures package from Bioconductor"
$metadata$genomeInfo$`Creation time`
[1] "2019-10-21 20:52:26 +0000 (Mon, 21 Oct 2019)"
$metadata$genomeInfo$`GenomicFeatures version at creation time`
[1] "1.37.4"
$metadata$genomeInfo$`RSQLite version at creation time`
[1] "2.1.2"
$metadata$genomeInfo$DBSCHEMAVERSION
[1] "1.2"
$class
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
>
> str(t1) #显示每个变量的行列数和类型
Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. ..@ values : Factor w/ 66 levels "chr1","chr2",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. ..@ lengths : int [1:30] 25139 32977 18919 23826 26471 20448 34789 19936 23361 18793 ...
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. ..@ start : int [1:410519] 4807788 4807823 4807830 4807892 4807896 4807898 4807911 4808237 4808455 4828584 ...
.. .. ..@ width : int [1:410519] 195 160 153 91 87 85 72 129 32 66 ...
.. .. ..@ NAMES : NULL
.. .. ..@ elementType : chr "ANY"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ...
.. .. ..@ lengths : int [1:48] 12327 12812 16807 16170 9829 9090 12035 11791 13416 13055 ...
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. ..@ seqnames : chr [1:66] "chr1" "chr2" "chr3" "chr4" ...
.. .. ..@ seqlengths : int [1:66] 195471971 182113224 160039680 156508116 151834684 149736546 145441459 129401213 124595110 130694993 ...
.. .. ..@ is_circular: logi [1:66] NA NA NA NA NA NA ...
.. .. ..@ genome : chr [1:66] "mm10" "mm10" "mm10" "mm10" ...
..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
.. .. ..@ rownames : NULL
.. .. ..@ nrows : int 410519
.. .. ..@ listData :List of 2
.. .. .. ..$ exon_id: int [1:410519] 18 19 20 21 22 23 24 25 26 27 ...
.. .. .. ..$ geneid : chr [1:410519] "18777" "18777" "18777" "18777" ...
.. .. ..@ elementType : chr "ANY"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ elementType : chr "ANY"
..@ metadata :List of 1
.. ..$ genomeInfo:List of 20
.. .. ..$ Db type : chr "TxDb"
.. .. ..$ Supporting package : chr "GenomicFeatures"
.. .. ..$ Data source : chr "UCSC"
.. .. ..$ Genome : chr "mm10"
.. .. ..$ Organism : chr "Mus musculus"
.. .. ..$ Taxonomy ID : chr "10090"
.. .. ..$ UCSC Table : chr "knownGene"
.. .. ..$ UCSC Track : chr "GENCODE VM23"
.. .. ..$ Resource URL : chr "http://genome.ucsc.edu/"
.. .. ..$ Type of Gene ID : chr "Entrez Gene ID"
.. .. ..$ Full dataset : chr "yes"
.. .. ..$ miRBase build ID : chr NA
.. .. ..$ transcript_nrow : chr "142446"
.. .. ..$ exon_nrow : chr "447558"
.. .. ..$ cds_nrow : chr "243727"
.. .. ..$ Db created by : chr "GenomicFeatures package from Bioconductor"
.. .. ..$ Creation time : chr "2019-10-21 20:52:26 +0000 (Mon, 21 Oct 2019)"
.. .. ..$ GenomicFeatures version at creation time: chr "1.37.4"
.. .. ..$ RSQLite version at creation time : chr "2.1.2"
.. .. ..$ DBSCHEMAVERSION : chr "1.2"
>
> class(t1)#: 查看变量类型，vector、data.frame、matrix、factor、list
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"
>
> mode(t1)#: 查看数据大类，character、numeric、logical
[1] "S4"
>
> typeof(t1)#: 查看数据细类，integer、double、single、float
[1] "S4"
==========================