BSgenome-utils(BSgenome)
BSgenome-utils()所属R语言包：BSgenome
BSgenome utilities
BSgenome公用事业
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Utilities for BSgenome objects.
公用事业为BSgenome对象。
用法----------Usage----------
## S4 method for signature 'BSgenome'
matchPWM(pwm, subject, min.score = "80%", exclude = "",
maskList = logical(0), asRangedData = TRUE)
## S4 method for signature 'BSgenome'
countPWM(pwm, subject, min.score = "80%", exclude = "",
maskList = logical(0))
## S4 method for signature 'BSgenome'
vmatchPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
with.indels = FALSE, fixed = TRUE, algorithm = "auto",
exclude = "", maskList = logical(0), userMask =
RangesList(), invertUserMask = FALSE, asRangedData = TRUE)
## S4 method for signature 'BSgenome'
vcountPattern(pattern, subject, max.mismatch = 0, min.mismatch = 0,
with.indels = FALSE, fixed = TRUE, algorithm = "auto",
exclude = "", maskList = logical(0), userMask =
RangesList(), invertUserMask = FALSE)
## S4 method for signature 'BSgenome'
vmatchPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
fixed = TRUE, algorithm = "auto", verbose = FALSE,
exclude = "", maskList = logical(0), asRangedData = TRUE)
## S4 method for signature 'BSgenome'
vcountPDict(pdict, subject, max.mismatch = 0, min.mismatch = 0,
fixed = TRUE, algorithm = "auto", collapse = FALSE,
weight = 1L, verbose = FALSE, exclude = "", maskList = logical(0))
参数----------Arguments----------
参数：pwm
A numeric matrix with row names A, C, G and T representing a Position Weight Matrix.
与行的数字矩阵命名A，C，G和T代表位置权重矩阵。
参数：pattern
A DNAString object containing the pattern sequence.
一个DNAString对象，其中包含的模式序列。
参数：pdict
A DNAStringSet object containing the pattern sequences.
一个DNAStringSet对象，其中包含的模式序列。
参数：subject
A BSgenome object containing the subject sequences.
一个BSgenome对象，其中包含的主题序列。
参数：min.score
The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "85%") of the highest possible score or as a single number.
计数匹配的最低得分。可以作为一个字符的字符串包含一个百分比（例如"85%"）可能达到的最高得分，或作为一个单一的数字。
参数：max.mismatch, min.mismatch
The maximum and minimum number of mismatching letters allowed (see ?`lowlevel-matching` for the details). If non-zero, an inexact matching algorithm is used.
数量最大和最小的不匹配，允许字母（?lowlevel-matching细节）。如果不为零，不精确的匹配算法。
参数：with.indels
If TRUE then indels are allowed. In that case, min.mismatch must be 0 and max.mismatch is interpreted as the maximum "edit distance" allowed between any pattern and any of its matches (see ?`matchPattern` for the details).
如果TRUE然后INDELS允许。在这种情况下，min.mismatch必须0和max.mismatch作为最大的“编辑距离”之间的任何模式和任何比赛所允许的解释（见?matchPattern详情）。
参数：fixed
If FALSE then IUPAC extended letters are interpreted as ambiguities (see ?`lowlevel-matching` for the details).
如果FALSE然后的IUPAC扩展字母解释为含糊之处（见?lowlevel-matching细节）。
参数：algorithm
For vmatchPattern and vcountPattern one of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", "shift-or", or "indels". For vmatchPDict and vcountPDict one of the following: "auto", "naive-exact", "naive-inexact", "boyer-moore", or "shift-or".
vmatchPattern和vcountPattern下列操作之一："auto"，"naive-exact"，"naive-inexact"，"boyer-moore"，"shift-or"或"indels"。对于vmatchPDict和vcountPDict下列操作之一："auto"，"naive-exact"，"naive-inexact"，"boyer-moore"或"shift-or"。
参数：collapse, weight
ignored arguments.
被忽略的参数。
参数：verbose
TRUE or FALSE.
TRUE或FALSE。
参数：exclude
A character vector with strings that will be used to filter out chromosomes whose names match these strings.
一个将用于筛选出染色体的名字相匹配这些字符串的字符串的字符向量。
参数：maskList
A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector.
命名的逻辑向量的首选用于与BSGenome对象时maskStates。口罩当使用bsapply功能，将会为美国在这个向量。
参数：userMask
A RangesList, containing a mask to be applied to each chromosome. See bsapply.
一个RangesList，含有被应用到每个染色体的面具。看到bsapply。
参数：invertUserMask
Whether the userMask should be inverted.
是否userMask应倒置。
参数：asRangedData
A logical value to assist in migrating output type from RangedData (deprecated) to GRanges. Should be FALSE. If TRUE, a warning message is issued and a RangedData object is returned.
一个逻辑值，以协助迁移输出型从RangedData（已过时）农庄。应该是FALSE。如果TRUE，一条警告消息发出和1 RangedData对象返回。
值----------Value----------
A GRanges object for matchPWM with two elementMetadata columns: "score" (numeric), and "string" (DNAStringSet).
一个农庄对象matchPWM两个elementMetadata列：“得分”（数字），“串”（DNAStringSet）的。
A GRanges object for vmatchPattern.
一个vmatchPattern农庄对象。
A GRanges object for vmatchPDict with one elementMetadata column: "index", which represents a mapping to a position in the original pattern dictionary.
一个农庄对象vmatchPDict一个elementMetadata列：“指数”，它代表一个映射到原有格局字典的地位。
A data.frame object for countPWM and vcountPattern with three columns: "seqname" (factor), "strand" (factor), and "count" (integer).
数据框对象countPWM和vcountPattern有三列：“seqname”（因子），“链”（因子），“伯爵”（整数）。
A DataFrame object for vcountPDict with four columns: "seqname" ('factor' Rle), "strand" ('factor' Rle), "index" (integer) and "count" ('integer' Rle). As with vmatchPDict the index column represents a mapping to a position in the original pattern dictionary.
一个DataFrame对象为vcountPDict四列：“seqname”（“因子”RLE），“链”（“因子”RLE），“索引”（整数）和“伯爵”（“整数“RLE）。至于以vmatchPDict索引列代表一个映射到原有格局字典的地位。
作者（S）----------Author(s)----------
P. Aboyoun
参见----------See Also----------
matchPWM, matchPattern, matchPDict, bsapply
matchPWM，matchPattern，matchPDict，bsapply
举例----------Examples----------
library(BSgenome.Celegans.UCSC.ce2)
data(HNF4alpha)
pwm <- PWM(HNF4alpha)
matchPWM(pwm, Celegans, asRangedData = FALSE)
countPWM(pwm, Celegans)
pattern <- consensusString(HNF4alpha)
vmatchPattern(pattern, Celegans, fixed = "subject", asRangedData = FALSE)
vcountPattern(pattern, Celegans, fixed = "subject")
vmatchPDict(HNF4alpha[1:10], Celegans, asRangedData = FALSE)
vcountPDict(HNF4alpha[1:10], Celegans)
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。
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发表于 2012-2-25 13:56:02
