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这是一个基于上一个问题（http://stackoverflow.com/questions/6538448/r-how-to-write-a-loop-to-get-a-matrix）的问题。

它与上一个不同，提供了更多细节，并根据 DWin 的注释提供了库和示例文件。所以，我将它作为一个新问题提交。你介意教我如何进一步修改这段代码吗？

要加载必要的库：

source("http://bioconductor.org/biocLite.R")
biocLite()

我的 protseq.fasta 文件包含以下内容：

>drugbank_target|1 Peptidoglycan synthetase ftsI (DB00303)  
MVKFNSSRKSGKSKKTIRKLTAPETVKQNKPQKVFEKCFMRGRYMLSTVLILLGLCALVARAAYVQSINADTLSNEADKR
SLRKDEVLSVRGSILDRNGQLLSVSVPMSAIVADPKTMLKENSLADKERIAALAEELGMTENDLVKKIEKNSKSGYLYLA
RQVELSKANYIRRLKIKGIILETEHRRFYPRVEEAAHVVGYTDIDGNGIEGIEKSFNSLLVGKDGSRTVRKDKRGNIVAH
ISDEKKYDAQDVTLSIDEKLQSMVYREIKKAVSENNAESGTAVLVDVRTGEVLAMATAPSYNPNNRVGVKSELMRNRAIT
DTFEPGSTVKPFVVLTALQRGVVKRDEIIDTTSFKLSGKEIVDVAPRAQQTLDEILMNSSNRGVSRLALRMPPSALMETY
QNAGLSKPTDLGLIGEQVGILNANRKRWADIERATVAYGYGITATPLQIARAYATLGSFGVYRPLSITKVDPPVIGKRVF
SEKITKDIVGILEKVAIKNKRAMVEGYRVGVKTGTARKIENGHYVNKYVAFTAGIAPISDPRYALVVLINDPKAGEYYGG
AVSAPVFSNIMGYALRANAIPQDAEAAENTTTKSAKRIVYIGEHKNQKVN
>drugbank_target|3 Histidine decarboxylase (DB00114; DB00117)  
MMEPEEYRERGREMVDYICQYLSTVRERRVTPDVQPGYLRAQLPESAPEDPDSWDSIFGDIERIIMPGVVHWQSPHMHAY
YPALTSWPSLLGDMLADAINCLGFTWASSPACTELEMNVMDWLAKMLGLPEHFLHHHPSSQGGGVLQSTVSESTLIALLA
ARKNKILEMKTSEPDADESCLNARLVAYASDQAHSSVEKAGLISLVKMKFLPVDDNFSLRGEALQKAIEEDKQRGLVPVF
VCATLGTTGVCAFDCLSELGPICAREGLWLHIDAAYAGTAFLCPEFRGFLKGIEYADSFTFNPSKWMMVHFDCTGFWVKD
KYKLQQTFSVNPIYLRHANSGVATDFMHWQIPLSRRFRSVKLWFVIRSFGVKNLQAHVRHGTEMAKYFESLVRNDPSFEI
PAKRHLGLVVFRLKGPNCLTENVLKEIAKAGRLFLIPATIQDKLIIRFTVTSQFTTRDDILRDWNLIRDAATLILSQHCT
SQPSPRVGNLISQIRGARAWACGTSLQSVSGAGDDPVQARKIIKQPQRVGAGPMKRENGLHLETLLDPVDDCFSEEAPDA
TKHKLSSFLFSYLSVQTKKKTVRSLSCNSVPVSAQKPLPTEASVKNGGSSRVRIFSRFPEDMMMLKKSAFKKLIKFYSVP
SFPECSSQCGLQLPCCPLQAMV
>drugbank_target|5 Glutaminase liver isoform, mitochondrial (DB00130; DB00142)  
MRSMKALQKALSRAGSHCGRGGWGHPSRSPLLGGGVRHHLSEAAAQGRETPHSHQPQHQDHDSSESGMLSRLGDLLFYTI
AEGQERTPIHKFTTALKATGLQTSDPRLRDCMSEMHRVVQESSSGGLLDRDLFRKCVSSSIVLLTQAFRKKFVIPDFEEF
TGHVDRIFEDVKELTGGKVAAYIPQLAKSNPDLWGVSLCTVDGQRHSVGHTKIPFCLQSCVKPLTYAISISTLGTDYVHK
FVGKEPSGLRYNKLSLDEEGIPHNPMVNAGAIVVSSLIKMDCNKAEKFDFVLQYLNKMAGNEYMGFSNATFQSEKETGDR
NYAIGYYHEEKKCFPKGVDMMAALDLYFQLCSVEVTCESGSVMAATLANGGICPITGESVLSAEAVRNTLSLMHSCGMYD
FSGQFAFHVGLPAKSAVSGAILLVVPNVMGMMCLSPPLDKLGNSHRGTSFCQKLVSLFNFHNYDNLRHCARKLDPRREGA
EIRNKTVVNLLFAAYSGDVSALRRFALSAMDMEQKDYDSRTALHVAAAEGHIEVVKFLIEACKVNPFAKDRWGNIPLDDA
VQFNHLEVVKLLQDYQDSYTLSETQAEAAAEALSKENLESMV
>drugbank_target|6 Coagulation factor XIII A chain (DB00130; DB01839; DB02340)  
SETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQ
SFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMY
VAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLY
VMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGV
FNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQ
ENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDT
YKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFY
TGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQ
VVGSDMTVTVQFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGE
LDVQIQRRPSM

要将数据加载到 R 进行分析，我已经完成了：

require("Biostrings")
data(BLOSUM100)
seqs <- readFASTA("./protseq.fasta", strip.descs=TRUE)

为了得到成对的数字，因为总共有 4 个序列，我已经完成了：

number <-c(1:4); dat <- expand.grid(number,number, stringsAsFactors=FALSE)
datr <- dat[dat[,1] > dat[,2] , ]

为了一一计算分数，我可以这样做：

 score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100, gapOpening=0, gapExtension=-5))

但是，我无法添加一个新列作为“分数”以包含每对蛋白质的所有分数。我试图这样做，但没有奏效。

datr$score <- lapply(datr, 1, function(i) { x <- datr[i,1]; y<- datr[i,2]; score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100, gapOpening=0, gapExtension=-5))})

您能介意评论如何进一步改进它吗？感谢 DWin 和 diliop 为我之前的问题提供了精彩的解决方案。

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1 回答 1

3

尝试：

datr$score <- sapply(1:nrow(datr), function(i) {
    x <- datr[i,1]
    y <- datr[i,2]
    score(pairwiseAlignment(seqs[[x]]$seq, seqs[[y]]$seq, substitutionMatrix=BLOSUM100,gapOpening=0, gapExtension=-5))
})

datr为了能够使用它们的名称更好地引用您的序列，您可能需要通过执行以下操作来整理：

colnames(datr) <- c("seq1id", "seq2id", "score")
datr$seq1name <- sapply(datr$seq1id, function(i) seqs[[i]]$desc)
datr$seq2name <- sapply(datr$seq2id, function(i) seqs[[i]]$desc)

或者，如果您只想提取加入 ID，即括号的内容，您可以stringr这样使用：

library(stringr)
datr$seq1name <- sapply(datr$seq2id, function(i) str_extract(seqs[[i]]$desc, "DB[0-9\\ ;DB]+"))

希望这可以帮助！

于 2011-07-01T04:07:48.600 回答