🧄R生物信息学统计分析
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R | 生物信息 | 定量 | edgeR | powsimR | GRanges | bumphunter | Alleliclmbalance | 遗传变异 | 蛋白质 | 基因 | 光谱分析 | Tidyverse | 统计数据可视化 | DNA
> dengueseq <- getncbiseq("NC_001477")
> dengueseq[1:50]
[1] "a" "g" "t" "t" "g" "t" "t" "a" "g" "t" "c" "t" "a" "c" "g" "t" "g" "g" "a"
[20] "c" "c" "g" "a" "c" "a" "a" "g" "a" "a" "c" "a" "g" "t" "t" "t" "c" "g" "a"
[39] "a" "t" "c" "g" "g" "a" "a" "g" "c" "t" "t" "g"
> getncbiseq <- function(accession)
{
require("seqinr") # this function requires the SeqinR R package
# first find which ACNUC database the accession is stored in:
dbs <- c("genbank","refseq","refseqViruses","bacterial")
numdbs <- length(dbs)
for (i in 1:numdbs)
{
db <- dbs[i]
choosebank(db)
# check if the sequence is in ACNUC database 'db':
resquery <- try(query(".tmpquery", paste("AC=", accession)), silent = TRUE)
if (!(inherits(resquery, "try-error")))
{
queryname <- "query2"
thequery <- paste("AC=",accession,sep="")
query(`queryname`,`thequery`)
# see if a sequence was retrieved:
seq <- getSequence(query2$req[[1]])
closebank()
return(seq)
}
closebank()
}
print(paste("ERROR: accession",accession,"was not found"))
}