msa(rphast)
msa()所属R语言包：rphast
MSA Objects
MSA对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creates a new MSA object given sequences.
创建一个新的MSA对象序列。
用法----------Usage----------
pointer.only=FALSE)
参数----------Arguments----------
参数：seqs
a character vector containing sequences, one per sample
字符向量序列，每一个样品
参数：names
a character vector identifying the sample name for each sequence. If NULL, use "seq1", "seq2", ...
字符向量确定每个序列的文件名了。如果NULL，使用“SEQ1”，“SEQ2”，...
参数：alphabet
a character string containing valid non-missing character states
一个字符串，其中包含有效的不可缺少的字符状态
参数：is.ordered
a logical indicating whether the alignment columns are stored in order. If NULL, assume columns are ordered.
逻辑指示是否对准列的顺序存储。如果为NULL，假定列进行排序。
参数：offset
an integer giving the offset of coordinates for the reference sequence from the beginning of the chromosome. The reference sequence is assumed to be the first sequence. Not used if is.ordered==FALSE.
一个整数，给出的偏移量从一开始的染色体中的参考序列的坐标。的参考序列被假定为第一序列。不使用如果is.ordered == FALSE。
参数：pointer.only
a boolean indicating whether returned alignment object should be stored by reference (see Details)
一个布尔值，指示是否返回的路线对象应存储的参考（见详情）
Details
详细信息----------Details----------
Make a new multiple sequence alignment (MSA) object given a vector of character strings. They can be optionally annotated with sample names.
一种新的多序列比对（MSA）一个字符串向量的对象。他们可以选择注明样品名称。
Each character string in seqs must be the same length, and number of elements in names (if provided) must match the number of elements in seqs.
每个字符在seqs串必须是相同的长度，和名称中的元素的数量（如果提供），必须匹配的数目元素seqs。
Alphabet generally does not have to be specified if working with DNA alignments.
一般不会有字母来指定，如果DNA比对工作。
About storing objects as pointers: If pointer.only==FALSE, the MSA object will be stored in R and can be viewed and modified by base R code as well as RPHAST functions. Setting pointer.only=TRUE will cause the object to be stored by reference, as an external pointer to an object created by C code. This may be necessary to improve performance, but the object can then only be viewed/manipulated via RPHAST functions. Furthermore, if an object is stored as a pointer, then its value is liable to be changed when passed as an argument to a function. All RPHAST functions which change the value of an external pointer make a note of this in the help pages for that function. For example, extract.feature.msa will alter an alignment if it is passed in as an external pointer (the argument will be changed into the return value). If this is undesireable, the copy.msa function can be used: extract.feature.msa(copy.msa(align)) will preserve the original alignment. Simple copying, ie, align2->align1 of objects stored as pointer will not behave like normal R objects: both objects will point to the same C structure, and both will be changed if either one
关于存储对象指针：如果pointer.only==FALSE，的MSA对象将被存储在R和碱基ŕ代码以及RPHAST的的功能，可以查看和修改。设置pointer.only=TRUE将导致对象被存储的参考，作为外部用C代码中创建的对象的指针。这可能是必要的，以提高性能，但对象可以被视为/ RPHAST功能通过操纵。此外，如果一个对象被存储为一个指针，那么它的价值是作为函数的参数传递时，可能会被改变。所有RPHAST功能改变的外部指针的值，记在该功能的帮助页面。例如，extract.feature.msa将改变对齐，如果它是通过在外部指针（参数将被改变成返回值）。如果这是不希望的，copy.msa功能可以用于：extract.feature.msa（copy.msa（对齐））将保存原始取向。简单的复制，即align2->align1的对象存储为指针不会像正常的R对象：两个对象指向同一个C结构，都将被改变：如果一个
（作者）----------Author(s)----------
Melissa J. Hubisz and Adam Siepel
实例----------Examples----------
# Here is an MSA object stored in the default mode[下面是一个MSA对象存储在默认模式]
m1 <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
names=c("human", "mouse", "rat"))
m2 <- m1
# NOTE seqs would not be directly accessible if stored by reference[注意seqs将不直接访问存储参考]
m2$seqs[3] <- "AAAAAA"
print(m1)
print(m1, print.seq=TRUE)
print(m2, print.seq=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 2012-9-28 00:00:29
