錯誤參數1不是矢量

Question

我在生物信息學的Little Book of R中找到了這個程序。鏈接：https://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter7.html

#finds start and stop codons in DNA sequence 
#from Avril Coghlan, Little Book of R for Bioinformatics 
library(Biostrings) 
findPotentialStartsAndStops <- function(sequence) 
{ 
    # Define a vector with the sequences of potential start and stop codons 
    codons <- c("ATG", "TAA", "TAG", "TGA") 
    # Find the number of occurrences of each type of potential start or  stop codon 
    for (i in 1:4) 
    { 
    codon <- codons[i] 
    # Find all occurrences of codon "codon" in sequence "sequence" 
    occurrences <- matchPattern(codon, sequence) 
    # Find the start positions of all occurrences of "codon" in sequence  "sequence" 
    codonpositions <- attr(occurrences,"start") 
    # Find the total number of potential start and stop codons in  sequence "sequence" 
    numoccurrences <- length(codonpositions) 
    if (i == 1) 
    { 
     # Make a copy of vector "codonpositions" called "positions" 
     positions <- codonpositions 
     # Make a vector "types" containing "numoccurrences" copies of  "codon" 
     types <- rep(codon, numoccurrences) 
    } 
    else 
    { 
     # Add the vector "codonpositions" to the end of vector "positions": 
     positions <- append(positions, codonpositions,  after=length(positions)) 
     # Add the vector "rep(codon, numoccurrences)" to the end of vector "types": 
     types <- append(types, rep(codon, numoccurrences),  after=length(types)) 
    } 
    } 
    # Sort the vectors "positions" and "types" in order of position along  the input sequence: 
    indices <- order(positions) 
    positions <- positions[indices] 
    types <- types[indices] 
    # Return a list variable including vectors "positions" and "types": 
    mylist <- list(positions,types) 
    return(mylist) 
} 

s1 <- "ACGGTATGTAATGTGA" 
#tried as vector also s1 <- c("A", "C", "G", "G", "T", "A", "T", "G", "T", "A", "A", "T", "G", "T", "G", "A") 

findPotentialStartsAndStops(s1) 

如果我使用DNA序列作爲字符串，我如果我使用的DNA序列作爲載體得到一個錯誤

Error in .Method(..., na.last = na.last, decreasing = decreasing) : 
     argument 1 is not a vector 
    7 .Method(..., na.last = na.last, decreasing = decreasing) 
    6 eval(expr, envir, enclos) 
    5 eval(.dotsCall, env) 
    4 eval(.dotsCall, env) 
    3 standardGeneric("order") 
    2 order(positions) 
    1 findPotentialStartsAndStops(s1) 
    Called from: (function() 
    { 
     .rs.breakOnError(TRUE) 
    })() 

，我得到一個錯誤

Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), : zero or more than one input sequence 
    8 .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), 
    width(solved_SEW), get_seqtype_conversion_lookup("B", seqtype), 
    PACKAGE = "Biostrings") 
    7 .charToXString(seqtype, x, start, end, width) 
    6 XString(NULL, subject) 
    5 XString(NULL, subject) 
    4 .XString.matchPattern(pattern, subject, max.mismatch, min.mismatch, 
    with.indels, fixed, algorithm) 
    3 matchPattern(codon, sequence) 
    2 matchPattern(codon, sequence) 
    1 findPotentialStartsAndStops(s1) 

從代碼中，程序似乎期望DNA序列是字符。

所以看起來也許問題是在該行 出現< - matchPattern（密碼子序列） 一些有關的輸入是一個矢量或者應該是一個矢量？但是密碼子已經是一個載體了，如果我要求課堂（密碼子），它就表現爲一個載體。我不明白什麼是錯的。

Answer 1

該代碼似乎已過時。當前版本的Biostrings（2.38.2）大概會返回一個與以前不同的對象。該生產線

codonpositions <- attr(occurrences,"start") 

應

codonpositions <- start(occurrences)