al2bp(seqinr)
al2bp()所属R语言包：seqinr
To Convert a forensic microsatellite allele name into its length in base pairs
要转换法医的微卫星等位基因的名字到它的长度，碱基对
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Conventions used to name forensic microsatellite alleles (STR) are described in Bar et al. (1994). The name "9.3" means for instance that there are 9 repetitions of the complete base oligomer and an incomplete repeat with 3 bp.
用来命名法医微卫星等位基因（STR）的约定在条形等。 （1994）。的名称为“9.3”的装置，例如，有9重复完整的基低聚物和用3 bp的一个不完整的重复。
用法----------Usage----------
al2bp(allele.name, repeat.bp = 4, offLadderChars = "><", split = "\\.")
参数----------Arguments----------
参数：allele.name
The name of the allele, coerced to a string type.
名称的等位基因，强制转换为一个字符串类型的。
参数：repeat.bp
The length in bp of the microsatellite base repeat, most of them are tetranucleotides so that it defaults to 4. Do not forget to change this to 5 for loci based on pentanucleotides such as Penta D or Penta E.
bp的碱基重复微卫星的长度，其中大部分是四核苷酸，这样它默认4。不要忘了这5位点的基础上pentanucleotides，如五D或五E.
参数：offLadderChars
NA is returned when at least one of these characters are found in the allele name. Off ladder alleles are typically reported as "<8" or ">19"
NA返回时被发现在这些字符中的至少一个等位基因名称。关闭阶梯等位基因，一般记为“<”或“> 19”
参数：split
The convention is to use a dot, as in "9.3", between the number of repeats and the number of bases in the incomplete repeat. On some locales where the decimal separator is a comma this could be a source of problem, try to use "," instead for this argument which is forwarded to strsplit.
惯例是使用重复的次数和在不完全重复的数目的碱基之间的一个点，在“9.3”，。在某些区域设置中的小数点分隔符是一个逗号，这可能是问题的来源，尝试使用“”，而不是被转发到strsplit这种说法。
Details
详细信息----------Details----------
Warnings generated by faulty numeric conversions are suppressed here.
在这里警告错误的数值转换所产生的抑制。
值----------Value----------
A single numeric value corresponding to the size in bp of the allele, or NA when characters spoting off ladder alleles are encountedred or when numeric conversion is impossible (e.g. with "X" or "Y" allele names at Amelogenin locus).
一个单一的数字值对应的碱基对的等位基因，或NA字符spoting阶梯等位基因encountedred或数字转换是不可能的（例如，使用“X”或“Y”Amelogenin基因座的等位基因的名字）的大小。
（作者）----------Author(s)----------
J.R. Lobry
参考文献----------References----------
DNA recommendations. 1994 report concerning further recommendations of the DNA Commission of the ISFH regarding PCR-based polymorphisms in STR (short tandem repeat) systems. Int. J. Leg. Med., 107:159-160.
参见----------See Also----------
identifiler for forensic microsatellite allele name examples.
identifiler法医微卫星等位基因的实例名称。
实例----------Examples----------
#[]
# Quality check and examples:[质量检查的例子：]
#[]
stopifnot( al2bp("9") == 36 ) # 9 repeats of a tetranucleotide is 36 bp[9的四核苷酸重复36基点]
stopifnot( al2bp(9) == 36 ) # also OK with numerical argument[数值参数也OK]
stopifnot( al2bp(9, 5) == 45 ) # 9 repeats of a pentanucleotide is 45 bp[9重复的核苷酸是45基点]
stopifnot( al2bp("9.3") == 39 ) # microvariant case[微变化情况]
stopifnot( is.na(al2bp("<8")) ) # off ladder case [从梯子上栽下的情况下]
stopifnot( is.na(al2bp(">19")) ) # off ladder case[从梯子上栽下的情况下]
stopifnot( is.na(al2bp("X")) ) # non STR case[非STR情况下，]
#[]
# Application to the alleles names in the identifiler data set where all loci are [设置所有位点的等位基因名在identifiler数据的应用是]
# tetranucleotide repeats:[四核苷酸重复序列：]
#[]
data(identifiler)
al.names <- unlist(identifiler)
al.length <- sapply(al.names, al2bp)
loc.names <- unlist(lapply(identifiler, names))
loc.nall <-unlist(lapply(identifiler, function(x) lapply(x,length)))
loc.fac <- factor(rep(loc.names, loc.nall))
par(lend = "butt", mar = c(5,6,4,1)+0.1)
boxplot(al.length~loc.fac, las = 1, col = "lightblue",
horizontal = TRUE, main = "Range of allele lengths at forensic loci",
xlab = "Length (bp)", ylim = c(0, max(al.length, na.rm = TRUE)))
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-9-30 01:13:42
