操作 GRanges 的集合

R 中的 Bioconductor 入門

Paula Andrea Martinez, PhD.

Data Scientist

GRangesList

GRangesList-class 是用來儲存一組 GRanges 的容器
- 適合高效儲存大量元素。
建立 GRangesList
- as(mylist, "GRangesList")
- GRangesList(myGranges1, myGRanges2, ...)
轉回 GRanges
- unlist(myGRangesList)
存取子 methods(class = "GRangesList")

何時使用清單？

多個 GRanges 物件可合併為一個 GRangesList
- 清單中的 GRanges 會視為較大物件的複合特徵
GRangesList 的常見情境：
- gene 的 transcripts
- transcript 的 exons
- read 對位
- 滑動視窗

# GRanges object with 983 genes 
hg_chrX

slidingWindows(hg_chrX, width = 20000, step = 10000)

# showing only two elements of the list
GRangesList object of length 983:
[[1]] 
GRanges object with 2 ranges and 0 metadata columns:
       seqnames           ranges strand 
         <Rle>        <IRanges>  <Rle>  
  [1]     chrX [276322, 296321]      +      
  [2]     chrX [286322, 303356]      +      
[[2]] 
GRanges object with 3 ranges and 0 metadata columns:
       seqnames           ranges strand 
  [1]     chrX [624344, 644343]      +      
  [2]     chrX [634344, 654343]      +      
  [3]     chrX [644344, 659411]      + 
...

GenomicFeatures 使用 transcript 資料庫（TxDb）物件來儲存中介資料、管理基因組位置，以及特徵與其識別碼之間的關係。

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
(hg <- TxDb.Hsapiens.UCSC.hg38.knownGene)

Db type: TxDb
Supporting package: GenomicFeatures
Data source: UCSC
Genome: hg38
Organism: Homo sapiens
Taxonomy ID: 9606
Resource URL: http://genome.ucsc.edu/
Type of Gene ID: Entrez Gene ID
transcript_nrow: 197782 
exon_nrow: 581036 
cds_nrow: 293052 
Db created by: GenomicFeatures package from Bioconductor
Creation time: 2016-09-29 13:02:09 +0000 (Thu, 29 Sep 2016)

Genes、transcripts、exons

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
hg <- TxDb.Hsapiens.UCSC.hg38.knownGene  #  hg is a A TxDb object

seqlevels(hg) <- c("chrX")               #  prefilter results to chrX

# transcripts
transcripts(hg, columns = c("tx_id", "tx_name"), filter = NULL)
# exons
exons(hg, columns = c("tx_id", "exon_id"), filter = list(tx_id = "179161"))

columns 與 filter 可為 NULL，或下列任一者：

"gene_id", "tx_id", "tx_name", "tx_chrom", "tx_strand", 
"exon_id", "exon_name", "exon_chrom", "exon_strand", 
"cds_id", "cds_name", "cds_chrom", "cds_strand" and "exon_rank"

依 transcript 分組的 exons

ABCD1 外顯子

hg <- TxDb.Hsapiens.UCSC.hg38.knownGene
seqlevels(hg) <- c("chrX")  #  prefilter chromosome X
exonsBytx <- exonsBy(hg, by = "tx")  #  exons by transcript

abcd1_179161 <- exonsBytx[["179161"]]  #  transcript id

width(abcd1_179161) # 每個外顯子的寬度，即圖中紫色區域

1299  181  143  169   95  146  146   85  126 1274

重疊（Overlaps）

# countOverlaps 回傳整數向量（計數）
countOverlaps(query, subject) 

# findOverlaps 回傳 Hits 物件
findOverlaps(query, subject) 

# subsetByOverlaps 回傳 GRangesList 物件
subsetByOverlaps(query, subject)

query 與 subject 可為 GRanges 或 GRangesList 物件。
重疊可以是完整或部分。

該你來實作了！

R 中的 Bioconductor 入門