R语言汇总LinkedPairs对象中的连接对PairSummaries()函数-中英文对照帮助文档
By MicroRbt Martinez PhD
R语言函数名：PairSummaries()
R语言函数功能：汇总LinkedPairs对象中的连接对
来自资源库：Bionconductor-software
PairSummaries()函数所属R语言包：所在R包具体名称、包功能的中英文双语描述见正文后面'--所在R语言包信息--'部分。
描述-----Description-----
Takes in a LinkedPairs object and gene calls, and returns a pairs list.
接收一个LinkedPairs对象和基因调用，并返回一个配对列表。
使用方法-----Usage-----
PairSummaries(SyntenyLinks,
GeneCalls,
DBPATH,
PIDs = TRUE,
IgnoreDefaultStringSet = FALSE,
Verbose = TRUE,
GapPenalty = TRUE,
TerminalPenalty = TRUE,
Model = "Global",
Correction = "none")
参数-----Arguments-----
参数SyntenyLinks介绍: A PairedLinks object.
一个PairedLinks对象。
参数GeneCalls介绍: A list of named DataFrames or GRanges objects. Dataframes built by "gffToDataFrame" can be used directly, while "GRanges" objects may also be used with limited functionality. Using a "GRanges" object will force all alignments to nucleotide alignments.
命名DataFrames或GRanges对象的列表。由“ gffToDataFrame”构建的数据帧可以直接使用，而“ GRanges”对象也可以有限的功能使用。使用“ GRanges”对象将强制所有比对变为核苷酸比对。
参数DBPATH介绍: A SQLite connection object or a character string specifying the path to the database file. Constructed from DECIPHER's Seqs2DB function.
一个SQLite连接对象或一个字符串，指定数据库文件的路径。从DECIPHER的Seqs2DB函数构造而成。
参数PIDs介绍: Logical indicating whether to perform pairwise alignments. If TRUE (the default) all pairs will be aligned using DECIPHER's AlignSeqs, or AlignTranslation function. This step can be time consuming, especially for large numbers of pairs.
逻辑指示是否执行成对对齐。如果TRUE（默认值），则所有对都将使用DECIPHER的AlignSeqs或AlignTranslation函数进行对齐。此步骤可能很耗时，尤其是对于大量对。
参数IgnoreDefaultStringSet介绍: Logical indicating alignment type preferences. If FALSE (the default) pairs that can be aligned in amino acid space will be aligned as an AAStringSet. If TRUE all pairs will be aligned in nucleotide space.
逻辑指示对齐类型首选项。如果可以在氨基酸空间中对齐的FALSEc（默认值）对将对齐为AAStringSet。如果TRUE所有对将在核苷酸空间中对齐。
参数Verbose介绍: Logical indicating whether or not to display a progress bar and print the time difference upon completion.
逻辑指示是否显示进度条并在完成时打印时差。
参数GapPenalty介绍: Argument passed to AlignTranslation
参数传递给AlignTranslation
参数TerminalPenalty介绍: Argument passed to AlignTranslation
参数传递给AlignTranslation
参数Model介绍: A character string specifying a model to use to identify pairs that are unlikely to be good orthologs. By default this is "Global", but two other models are included; "Local" and "Exact", which have minor differences in performance. Alternatively, a user generated model can be used.
字符串，指�
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发表于 2021-2-21 10:57:19
