R语言 rphast包 rphast-package()函数中文帮助文档(中英文对照)

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rphast-package(rphast)
rphast-package()所属R语言包：rphast

                                         R interface to PHAST software for comparative genomics
                                         R接口PHAST软件比较基因组学

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

RPHAST is an R interface to the PHAST pacakge (Phylogenetic Analyis with Space/Time Models).  It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models.  It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.
RPHAST是一个R接口的PHAST线路咨询（时间/空间模型的系统发育Analyis）的。它可用于多种类型的比较和进化基因组学的分析，如从序列数据估计模型的演进，保护或加速得分的路线，和预测的基础上保护或自定义的系统发育隐马尔可夫模型的元素。它也可以执行许多基本的操作，多序列比对和系统进化树。


Details

详细信息----------Details----------

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Index: <pre> [.msa   Extract, replace, reorder MSA... add.UTRs.feat   Add UTRs to features... add.alt.mod     Add a lineage-specific model... add.introns.feat        Add introns to features... add.signals.feat        Add start/stop codon, 3'/5' splice signals to         features... alphabet.msa    MSA Alphabet apply.bgc.sel   Apply bgc+selection parameters to a matrix... as.data.frame.feat      Features to Data Frame as.list.tm      Tree Model to List as.pointer.feat Features To Pointer as.pointer.msa  MSA To Pointer as.track.feat   Create a features track... as.track.msa    Create an alignment track... as.track.wig    Create a wig track... base.freq.msa   Get the frequencies of characters in an         alignment... bgc.sel.factor  BGC+selection factor... branchlength.tree       Get the total length of the edges of a tree... codon.clean.msa Clean an alignment for codon analysis... col.expected.subs.msa   Obtain expected number of substitutions on each         branch for each site... complement      complement composition.feat        Composition of features with respect to         annotations... concat.msa      Concatenate msa objects... coord.range.msa Obtain the range of coordinates in a MSA         objects... copy.feat       Features copy copy.msa        MSA copy coverage.feat   Features coverage... density.feat    Features kernel density... depth.tree      Get the distance from a node to the root of a         tree... dim.feat        Feature dimensions dim.msa         Returns the dimensions of an msa object as (#         of species, # of enrichment.feat Enrichment of features with respect to         annotation types... expected.subs.msa       Obtain expected number of substitutions on each         branch and site... extract.feature.msa     Extract features from an MSA object... feat    Features Objects fix.semicolon.tree      Add a semi-colon to end of tree string... fix.start.stop.feat     Fix start and stop signals... from.pointer.msa        MSA From Pointer gc.content.msa  Get the fraction of G's and C's in an         alignment... get.rate.matrix.params.tm         Get the parameters describing a rate matrix... get4d.msa       Extract fourfold degenerate sites from an MSA         object... guess.format.msa        MSA Format From Filename Extension hist.feat       plot histogram of feature lengths... hmm     Create an rphast HMM object informative.regions.msa         Get informative regions of an alignment... inverse.feat    Get inverse features... is.format.msa   Check an MSA Format String is.msa  Check an MSA object... is.ordered.msa  MSA is Ordered? is.subst.mod.tm Check Substitution Model Strings is.tm   Tree Models is.track        Is this a track? label.branches  Label tree branches label.subtree   Label subtree likelihood.msa  MSA Likelihood mod.backgd.tm   Adjust tree model background frequencies while         maintaining msa     MSA Objects name.ancestors  Name Ancestral Nodes names.msa       MSA Sequence Names ncol.feat       Number of Columns in Features ncol.msa        MSA Sequence Length. ninf.msa        The number of informative columns in an         alignment... nrow.feat       Number of Features nrow.msa        MSA Number of Sequences nstate.hmm      HMM number of states... numleaf.tree    Number of leaves in a Tree numnodes.tree   Number of Nodes in a Tree offset.msa      MSA Index Offset overlap.feat    Feature overlap... pairwise.diff.msa       Get pairwise differences per site between         sequences... phastCons       Produce conservation scores and identify         conserved elements,... phyloFit        Fit a Phylogenetic model to an alignment... phyloP  phyloP (basewise or by feature) phyloP.prior    phyloP prior phyloP.sph      phyloP SPH plot.altmodel.tm        Make a bubble plot of a lineage-specific         transition matrix of a... plot.feat       Features plot plot.gene       Gene plot plot.msa        Plot an alignment... plot.rate.matrix        Make a bubble plot of a transition matrix... plot.tm         Make a bubble plot of the transition matrix for         a tree model. plot.track      Make browser-like plot in rphast... postprob.msa    Obtain posterior probilities of every state at         every node... print.feat      Printing a features Object print.msa       Printing MSA objects print.tm        Printing Tree Models prune.tree      Prune a Tree range.feat      Features range range.track     Get the coordinate range of a list of RPHAST         results... rbind.feat      concatenate feature objects... read.feat       Read a Feature File (GFF, BED, or GenePred) read.hmm        Read an HMM object from a file... read.msa        Reading an MSA Object read.newick.tree        Read a Newick Tree from a File read.tm         Read a Tree Model rename.tree     Tree Node Renaming rescale.tree    Scale a Tree or Subtree reverse.complement.msa         Reverse complement a multiple sequence         alignment... sample.msa      Sample columns from an MSA... score.hmm       Score an alignment using a general phylo-HMM set.rate.matrix.tm      Set the rate matrix of a tree model using         model-specific parameters. simulate.msa    Simulate a MSA given a tree model and HMM. smooth.wig      Smooth a wig plot in rphast... sort.feat       Sort a GFF... split.by.feature.msa    Split an MSA by feature... split.feat      Split features by length... state.freq.msa  Get the observed frequencies of states in an         alignment... strip.gaps.msa  MSA Strip Gaps sub.msa         MSA Subset subst.mods      List PHAST Substitution Models subtree         Subtree summary.feat    Features Summary summary.msa     MSA Summary summary.tm      Tree Model Summary summary.tree    Get a summary of a Newick-formatted tree, edge         lengths, node names, tagval  Extract value from tag-value formatted         attributes... tagval.feat     Extract value from tag-value formatted         attribute in features object... tm      Tree Models total.expected.subs.msa         Obtain expected number of substitutions on each         branch... translate.msa   Get amino acid sequences from an alignment... unapply.bgc.sel Unapply bgc+selection parameters from a         matrix... unique.feat     Remove overlapping genes... write.feat      Writing a features Object write.hmm       Write an HMM object to a file... write.msa       Writing MSA Objects to Files write.tm        Wrting Tree Models </pre>
指数：<PRE>。MSA提取，替换，重新排序MSA ... add.UTRs.feat添加非编码区的功能... add.alt.mod添加的血统，具体型号... add.introns.feat内含子功能... add.signals.feat添加启动/停止密码子，3/ 5剪接位信号的功能... alphabet.msa MSA的字母apply.bgc.sel应用BGC +选择参数矩阵... as.data.frame.feat数据框as.list.tm树模型的功能列表as.pointer.feat的特点为指针as.pointer.msa的MSA为指针as.track.feat创建一个功能跟踪... as.track.msa创建对齐轨道... as.track.wig创建一个假发轨... base.freq.msa如何在一个对准的字符的频率... bgc.sel.factor BGC +的选择因素... branchlength.tree获取一棵树的边缘的总长度... codon.clean.msa清洁密码分析的对齐方式... col.expected.subs.msa取得预期的替换每个分支上的每个站点...补充补充注解功能composition.feat组成的... concat.msa并置MSA对象... coord.range.msa获取在MSA对象的范围内的坐标... copy.feat的特色副本copy.msa MSA复制coverage.feat功能覆盖... density.feat功能的内核密度... depth.tree从一个节点到树根的距离...尺寸dim.feat的特征尺寸dim.msa返回的MSA对象的（＃种，注释类型＃的enrichment.feat的富集功能expected.subs.msa取得预期换人，每个分支和网站... extract.feature.msa的特征提取，从MSA对象的壮举对象fix.semicolon.tree添加一个分号结束字符串的树... fix.start.stop.feat修复的开始和停止信号... from.pointer.msa MSA从指针gc.content.msa取得的分数的G和C的比对... get.rate.matrix.params.tm的速度矩阵参数... get4d.msa提取四倍退化网站从MSA对象... guess.format.msa MSA格式从文件名扩展hist.feat“图直方图特征长度...嗯创建一个rphast的HMM的对象informative.regions.msa获取信息的区域对齐方式... inverse.feat逆的功能... is.format.msa检查MSA格式字符串is.msa检查MSA对象... is.ordered.msa MSA是有序的吗？is.subst.mod.tm检查替代模型的字符串is.tm树模型is.track这是一首曲目，？label.branches标签树的分支label.subtree标签的子树likelihood.msa MSA的可能性mod.backgd.tm树模型的背景频率调整，同时保持MSA MSA对象的名称。祖先的名字氏宗祠节点names.msa MSA序列名称ncol.feat的特点ncol.msa MSA序列长度的列数。ninf.msa的信息列在对齐方式... nrow.feat号码，的特点nrow.msa MSA号码的的序列nstate.hmm HMM的状态数... numleaf.tree的叶子在一个的树numnodes.tree数，在一个树offset.msa的MSA指数偏移overlap.feat功能重叠的节点数目... pairwise.diff.msa取得成对每个站点之间的序列差异phastCons产生保护成绩，并确定保留下来的元素，... phyloFit装一个系统发育模型比对... phyloP phyloP（basewise或功能）phyloP.prior phyloP前phyloP.sph phyloP SPH plot.altmodel.tm制作的系特异性转移矩阵... plot.feat特点图plot.gene基因图plot.msa图对准... plot.rate.matrix一个气泡图气泡图过渡矩阵... plot.tm一个气泡图的过渡矩阵的树模型。plot.track浏览器般的图在rphast ... postprob.msa的每一个国家的每一个节点获取后probilities print.feat打印一个的对象特点print.msa印刷MSA对象print.tm印刷树模型prune.tree修剪一个的树range.feat特点范围range.track的坐标范围的列表RPHAST结果... rbind.feat CONCATENATE功能的对象... read.feat阅读一个特征文件（GFF，床上或GenePred的）read.hmm HMM对象从一个文件... read.msa读MSA对象read.newick.tree阅读将Newick树从一个的文件read.tm阅读树模型rename.tree树节点重命名rescale.tree规模的Tree或子树reverse.complement.msa的反向补充多序列比对... sample.msa样品列从MSA ...得分。嗯分数对齐使用一般phylo-HMM set.rate.matrix.tm率矩阵的树模型，使用模型的具体参数设置。simulate.msa模拟MSA树模型和HMM的。smooth.wig顺利假发图rphast ... sort.feat排序一个GFF分割的split.by.feature.msa MSA功能... split.feat分割功能的长度... state.freq.msa获取所观察到的频率对齐状态... strip.gaps.msa MSA带跳空sub.msa MSA子集subst.mods列表PHAST替代模型的子树子树summary.feat功能摘要summary.msa MSA摘要summary.tm树模型的总结summary.tree获取将Newick格式的树边的长度，节点名称，标签值格式化属性值的tagval提取物... tagval.feat提取值标记值的格式属性，对象特点的总结... TM树模型total.expected。 subs.msa获取每个分支上的预期数的取代... translate.msa获取的氨基酸序列从一个对准... unapply.bgc.sel撤消核销BGC +选择参数从一个矩阵... unique.feat移除重叠基因。 .. write.feat编写一个功能对象write.hmm写HMM对象到一个文件... write.msa MSA对象写入到文件write.tm Wrting树模型</ pre>

Further information is available in the following vignettes:
进一步的信息可以在下面的小插曲：

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（作者）----------Author(s)----------



Melissa Hubisz, Katherine Pollard, and Adam Siepel


Maintainer: Melissa Hubisz &lt;mjhubisz@cornell.edu&gt;


转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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