PH525.4x第二周内容围绕GRange类的操作和使用Annotation进行数据关联两个主题展开，并展示了几个比较“炫”的功能。由于内容繁多，信息量大，故笔记之以便日后参考。
该课程的演示数据为ChIP-seq的实验数据，背景为人类肝细胞（cell line：HepG2和GM12878）中被ESRRA （estrogen related receptor alpha）绑定的基因片段。
在展示数据操作之前，首先检查bioconductor的版本号，不同版本的输出可能存在差异。
library(BiocInstaller) biocVersion() #[1] ‘3.0’
载入演示数据：
library(devtools)
install_github("genomicsclass/ERBS")
library(ERBS)
data(GM12878)
data(HepG2)
class(HepG2)
#[1] "GRanges"
#attr(,"package")
#[1] "GenomicRanges"
HepG2
# GRanges object with 303 ranges and 7 metadata columns:
# seqnames ranges strand | name score col signalValue pValue
# <Rle> <IRanges> <Rle> | <numeric> <integer> <logical> <numeric> <numeric>
# [1] chr2 [ 20335378, 20335787] * | <NA> 0 <NA> 58.251 75.899
# [2] chr20 [ 328285, 329145] * | <NA> 0 <NA> 10.808 69.685
# [3] chr6 [168135432, 168136587] * | <NA> 0 <NA> 17.103 54.311
# [4] chr19 [ 1244419, 1245304] * | <NA> 0 <NA> 12.427 43.855
# [5] chr11 [ 64071828, 64073069] * | <NA> 0 <NA> 10.85 40.977
# ... ... ... ... ... ... ... ... ... ...
# [299] chr4 [ 1797182, 1797852] * | <NA> 0 <NA> 9.681 10.057
# [300] chr1 [110198573, 110199126] * | <NA> 0 <NA> 7.929 10.047
# [301] chr17 [ 17734052, 17734469] * | <NA> 0 <NA> 5.864 9.99
# [302] chr1 [ 48306453, 48306908] * | <NA> 0 <NA> 5.66 9.948
# [303] chr12 [123867207, 123867554] * | <NA> 0 <NA> 13.211 9.918
# qValue peak
# <numeric> <integer>
# [1] 6.143712e-72 195
# [2] 5.028065e-66 321
# [3] 7.930665e-51 930
# [4] 1.359756e-40 604
# [5] 7.333863e-38 492
# ... ... ...
# [299] 1.423343e-08 402
# [300] 1.442076e-08 197
# [301] 1.638918e-08 227
# [302] 1.799414e-08 211
# [303] 1.921805e-08 163
# -------
# seqinfo: 93 sequences (1 circular) from hg19 genome
我们可以看见该HepG2数据有3个column为位置信息，7个为特征信息（metadata column）。我们可以直接使用granges提取所有位置信息或seqnames，ranges，strand提取相关信息，并支持IRanges操作，譬如start，end，width等；使用values或mcols函数可以提取metadata；提取row的方法同dataframe类操作或使用chr=="xxx"的形式索引。值得注意的是seqnames的输出并不是character类，有character需求的话需要转换。同时seqnames按原始order计算染色体位置出现频率，即同一个染色体位置如果分开于不相邻的row按不同染色体位置计数，需要直接计算每一个染色体位置出现的频率可以对原始数据order以后再提取或使用table函数。
seqnames(HepG2) # factor-Rle of length 303 with 292 runs # Lengths: 1 1 1 1 1 1 1 1 ... 1 1 1 1 1 1 1 # Values : chr2 chr20 chr6 chr19 chr11 chr20 chr19 chr2 ... chr17 chr3 chr4 chr1 chr17 chr1 chr12 # Levels(93): chr1 chr2 chr3 chr4 chr5 ... chrUn_gl000246 chrUn_gl000247 chrUn_gl000248 chrUn_gl000249 seqnames(HepG2[order(HepG2)]) # factor-Rle of length 303 with 23 runs # Lengths: 18 38 15 4 8 24 14 11 ... 21 6 16 27 3 5 4 # Values : chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 ... chr17 chr18 chr19 chr20 chr21 chr22 chrX # Levels(93): chr1 chr2 chr3 chr4 chr5 ... chrUn_gl000246 chrUn_gl000247 chrUn_gl000248 chrUn_gl000249
与GRanges类相关的是IRanges类的操作，以下代码一图读懂基本操作~
ir <- IRanges(5,10)
# set up a plotting window so we can look at range operations
plot(0,0,xlim=c(0,23),ylim=c(0,13),type="n",xlab="",ylab="",xaxt="n")
axis(1,0:15)
abline(v=0:14 + .5,col=rgb(0,0,0,.5))
# plot the original IRange
plotir <- function(ir,i) { arrows(start(ir)-.5,i,end(ir)+.5,i,code=3,angle=90,lwd=3) }
plotir(ir,1)
# draw a red shadow for the original IRange
polygon(c(start(ir)-.5,start(ir)-.5,end(ir)+.5,end(ir)+.5),c(-1,15,15,-1),col=rgb(1,0,0,.2),border=NA)
# draw the different ranges
plotir(shift(ir,-2), 2)
plotir(narrow(ir, start=2), 3)
plotir(narrow(ir, end=5), 4)
plotir(flank(ir, width=3, start=TRUE, both=FALSE), 5)
plotir(flank(ir, width=3, start=FALSE, both=FALSE), 6)
plotir(flank(ir, width=3, start=TRUE, both=TRUE), 7)
plotir(ir * 2, 8)
plotir(ir * -2, 9)
plotir(ir + 2, 10)
plotir(ir - 2, 11)
plotir(resize(ir, 1), 12)
text(rep(15,12), 1:12, c("ir","shift(ir,-2)","narrow(ir,start=2)",
"narrow(ir,end=5)",
"flank(ir, start=T, both=F)",
"flank(ir, start=F, both=T)",
"flank(ir, start=T, both=T)",
"ir * 2","ir * -2","ir + 2","ir - 2",
"resize(ir, 1)"), pos=4)
GRanges类是IRanges类的拓展，除了IRanges类的基本特征之外，还需要提供染色体位置seqnames和正链还是反链strand两个关键信息（strand默认为“+”）。c函数可以合并两个GRanges类，gaps可以寻找未被原始序列覆盖的序列（补集），disjoint可以将原始序列分割成互不相交的序列，reduce输出整个序列覆盖的范围和gaps互补。%over%命令，如"HepG2 %over% GM12878"，可以生成长度为HepG2长度的逻辑向量判断HepG2的各序列是否与GM12878存在交集。值得一提的是findOverlaps函数，输出Hits类对象：
fo <- findOverlaps(HepG2, GM12878) fo # Hits of length 75 # queryLength: 303 # subjectLength: 1873 # queryHits subjectHits # <integer> <integer> # 1 1 12 # 2 2 78 # 3 4 777 # 4 5 8 # 5 8 13 # ... ... ... # 71 285 621 # 72 287 174 # 73 291 1855 # 74 294 512 # 75 300 144 queryHits(fo) subjectHits(fo)
queryHits输出在HepG2中与GM12878重叠的序列，subjectHits反之。当然也可以用%over%。
HepG2 %over% GM12878 HepG2[HepG2 %over% GM12878]
除了findOverlaps，还可以使用distanceToNearest函数找到最近序列，输出类似findOverlaps，distance可以输出距离值。
distanceToNearest(HepG2[17],GM12878) # Hits of length 1 # queryLength: 1 # subjectLength: 1873 # queryHits subjectHits distance # <integer> <integer> <integer> # 1 1 945 2284 mcols(d)$distance
当然这里所有的操作都需要注意strand方向。
接着就看看我们的ERBS究竟绑了些什么基因。载入基因注释（annotation）数据Homo.sapiens并查看基因信息。
library(Homo.sapiens) ghs = genes(Homo.sapiens) genome(ghs)
我们捕捉在两种cell line，HepG2和GM12878，ERBS绑定一致的区域。
res = findOverlaps(HepG2,GM12878) erbs = HepG2[queryHits(res)] erbs = granges(erbs)
#Another way
erbs = intersect(HepG2, GM12878)
precede函数可以找出转录起始端在绑定位置上游的基因。
index <- precede(erbs, subject = ghs) ghs[index,]
更好的做法是首先对ghs使用resize函数收集转录起始端位置，再使用distanceToNearest函数，可以找出绑定位置即为转录起始端的基因和对距离进行筛选（precede命令不能做到）。
tssge <- resize(ghs, 1) d <- distanceToNearest(erbs, tssge) queryHits(d) dist <- values(d)$distance index <- subjectHits(d)[dist < 1000] tssge[index,] # GRanges object with 41 ranges and 1 metadata column: # seqnames ranges strand | GENEID # <Rle> <IRanges> <Rle> | <IntegerList> # 80023 chr20 [ 327370, 327370] + | 80023 # 2101 chr11 [ 64073044, 64073044] + | 2101 # 7086 chr3 [ 53290130, 53290130] - | 7086 # 5478 chr7 [ 44836241, 44836241] + | 5478 # 286262 chr9 [140095163, 140095163] - | 286262 # ... ... ... ... ... ... # 55090 chr17 [ 17380300, 17380300] + | 55090 # 11165 chr6 [ 34360457, 34360457] - | 11165 # 56181 chr1 [ 26146397, 26146397] + | 56181 # 347734 chr6 [ 44225283, 44225283] - | 347734 # 2948 chr1 [110198698, 110198698] + | 2948 # ------- # seqinfo: 93 sequences (1 circular) from hg19 genome
使用select函数对Homo.sapiens进行注释查询，select参数包括查询数据库，keys和对应的key type（关联注释的关键）及注释column。
首先我们看Homo.sapiens支持的key type。
keytypes(Homo.sapiens) # [1] "GOID" "TERM" "ONTOLOGY" "DEFINITION" "ENTREZID" "PFAM" # [7] "IPI" "PROSITE" "ACCNUM" "ALIAS" "CHR" "CHRLOC" # [13] "CHRLOCEND" "ENZYME" "MAP" "PATH" "PMID" "REFSEQ" # [19] "SYMBOL" "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" "GENENAME" # [25] "UNIPROT" "GO" "EVIDENCE" "GOALL" "EVIDENCEALL" "ONTOLOGYALL" # [31] "OMIM" "UCSCKG" "GENEID" "TXID" "TXNAME" "EXONID" # [37] "EXONNAME" "CDSID" "CDSNAME"
我们使用GENEID进行关联，关联注释选择“SYMBOL”和“GENENAME”。注意keys一般接受character输入，需要转换。
res <- select(Homo.sapiens, keys = as.character(values(tssge[index, ])$GENEID), keytype = "GENEID", columns = c("SYMBOL", "GENENAME"))
head(res)
# GENEID SYMBOL GENENAME
# 1 80023 NRSN2 neurensin 2
# 2 2101 ESRRA estrogen-related receptor alpha
# 3 7086 TKT transketolase
# 4 5478 PPIA peptidylprolyl isomerase A (cyclophilin A)
# 5 286262 TPRN taperin
# 6 79696 ZC2HC1C zinc finger, C2HC-type containing 1C
接着查找绑定的序列（motif），需要载入人类基因组数据库。注意在这里载入Hsapines数据和载入BSgenome.Hsapiens.UCSC.hg19是一样的（不是载入包，而是数据！）。提取单条染色体基因可以使用$。
library(BSgenome.Hsapiens.UCSC.hg19) Hsapines # Human genome # | # | organism: Homo sapiens (Human) # | provider: UCSC # | provider version: hg19 # | release date: Feb. 2009 # | release name: Genome Reference Consortium GRCh37 # | 93 sequences: # | chr1 chr2 chr3 chr4 # | chr5 chr6 chr7 chr8 # | chr9 chr10 chr11 chr12 # | chr13 chr14 chr15 chr16 # | chr17 chr18 chr19 chr20 # | ... ... ... ... # | chrUn_gl000233 chrUn_gl000234 chrUn_gl000235 chrUn_gl000236 # | chrUn_gl000237 chrUn_gl000238 chrUn_gl000239 chrUn_gl000240 # | chrUn_gl000241 chrUn_gl000242 chrUn_gl000243 chrUn_gl000244 # | chrUn_gl000245 chrUn_gl000246 chrUn_gl000247 chrUn_gl000248 # | chrUn_gl000249 # | (use ‘seqnames()‘ to see all the sequence names, use the ‘$‘ or ‘[[‘ operator to access a given # | sequence)
getSeq命令可以输出目标位置的基因序列以便对其进一步分析。
hepseq <- getSeq(Hsapiens, erbs) # A DNAStringSet instance of length 75 # width seq # [1] 410 GAGACAGGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCTGA...GAAGGAGATGCAACCTTCCAGGAAGCAGAAATGTTCAAGGACTCTC # [2] 861 TGGGAAGGACACAACTGAATGAGGCTGTGCAGAGGCGACAGATTCC...CCGTGTGACTCCAAGCAGAACCTCCAACCGTGTGTGTGTGTGTGTG # [3] 886 GTGAAGGCCCTGGAGTAGGCGGTGCGTACCCGGTGTCCCGAGGCCC...GTGCCGAATCTGCAGTGTTTTTGGCACCTCCGTGGGCACCTAGGCT # [4] 1242 CATCCTCCACCTTAACACTCAGCACCCTTAGAGATGCAAAGTTCCC...GGCCGCGATGTCCTTTTGTGTCCTACAAGCAGCCGGCGGCGCCGCC # [5] 477 AGGAATGAGCACCCACGGAGAAATGCAGTCCCGACCCCTTCCACCC...GTGATTGGACAAGGATGGTCAAAATGTATCCTTCTGGAATCTGAGC # ... ... ... # [71] 429 TGAGCCCCAACAAAACAAAAAAGCCAATCCTGCTGGTCTAAACTGG...CCATTCAACAAAGCACAGTATGCACCATGCAGTATTTTCTTGTGAT # [72] 551 GTGGCGGAAGGAAGCGGCGCGCTTGGCCGCCAGGAGCCGCTTGCGC...CAGACAAGGTCCAGGGACCTGGCGGCTGAGGGGACCCTCAAGGCTC # [73] 805 TACCAGGCCGAGGGATCTCCAAACGCAGCCAACTCCTCCCGGGGAC...GGAGAGGGTCCGCGCGGGTCTCCGGCCACTGCTGCGCGCGGCAAAG # [74] 1037 ATCCCCTCCGCCCTCCAGAGGGGACCACACTGGAGTAGTGCCCGGA...CGAGGCTCTACATGGCCTCGCCCGCGTTCCTCGCCCACTCACTCGC # [75] 554 TCCGGAGAAGAAGAAACGGGGGAAGAACTTTTCTCTTACGATCTGG...CGCGTGGGCGGGAAGTGCCGAGCGGCTGGGGACCGGCTCTAGGGAC
使用countPattern，vcountPattern，alphabetFrequency等函数可对某种pattern在序列中的出现进行统计分析。
vcountPattern("GC", hepseq)
# [1] 34 75 94 139 28 52 47 79 9 109 187 58 32 21 113 18 23 83 110 58 142 33 106 40 89
# [26] 24 22 116 64 25 91 128 58 19 38 101 42 89 85 68 23 184 88 58 38 138 56 40 23 83
# [51] 101 90 43 20 47 104 62 71 133 62 144 67 42 119 82 127 78 27 47 99 22 64 98 121 51
待续...
HarvardX: PH525.4x Introduction to Bioconductor第二周笔记
原文：http://www.cnblogs.com/nutastray/p/4416020.html