R语言 R453Plus1Toolbox包 SFFRead-class()函数中文帮助文档(中英文对照)

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SFFRead-class(R453Plus1Toolbox)
SFFRead-class()所属R语言包：R453Plus1Toolbox

                                        Class "SFFRead"
                                         类“SFFRead”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is a container for a single read from files in Roche's Standard Flowgram Format (SFF).
这个类是一个单一从罗氏的标准Flowgram的格式（SFF）的文件的只读的容器。


类的对象----------Objects from the Class----------

Objects can be created by calls of the form new("SFFRead", ...). Usually, objects will be created by calling the getRead method on an object of class SFFContainer.
创建对象可以通过检测的形式new("SFFRead", ...)。通常，对象将被创建，通过调用一个对象类getReadSFFContainer方法。


插槽----------Slots----------




name: Object of class "character" representing the name of the read.
name：Object类的"character"代表读的名字。




read: Object of class "DNAString" containing the basecalled
read：Object类的"DNAString"包含的basecalled的




flowgramFormat: Object of class "numeric" representing the format used to  encode each of the flowgram values for each read. Currently, only one flowgram format has been
flowgramFormat：Object类的"numeric"代表用于编码每个每读的flowgram值的格式。目前，只有一个flowgram格式已




flowChars: Object of class "character" containing the array of nucleotide  bases ('A', 'C', 'G', 'T') that correspond to the nucleotides used for each flow of each
flowChars：对象类"character"包含数组对应每个每个流的核苷酸碱基（“A”，“C”，“G”，“T”）




keySequence: Object of class "character" representing the nucleotide bases
keySequence：Object类的"character"代表的碱基




clipQualityLeft: Object of class "numeric" representing the position of the  first base after the clipping point for an attached quality sequence. If only a combined  (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no
clipQualityLeft：Object类的"numeric"代表的附加质量序列的剪裁点后的第一个碱基的位置。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityLeft。如果没有




clipQualityRight: Object of class "numeric" representing the position of  the last base before the clipping point for an attached quality sequence. If only a combined  (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no
clipQualityRight：Object类的"numeric"代表剪裁点前附加质量序列的最后一个碱基的位置。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityRight。如果没有




clipAdapterLeft: Object of class "numeric" representing the position of the  first base after the clipping point for an attached adapter sequence. If only a combined  (quality+adapter) clipping position is computed it should be stored in clipQualityLeft. If no
clipAdapterLeft：Object类的"numeric"代表一个附加适配器序列的剪裁点后的第一个碱基的地位。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityLeft。如果没有




clipAdapterRight: Object of class "numeric" representing the position of  the last base before the clipping point for an attached adapter sequence. If only a combined  (quality+adapter) clipping position is computed it should be stored in clipQualityRight. If no
clipAdapterRight：Object类的"numeric"代表的剪裁点前的最后一个附加适配器序列碱基的地位。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityRight。如果没有




flowgram: Object of class "numeric" containing the homopolymer stretch
flowgram：Object类的"numeric"含有均聚物的拉伸




flowIndexes: Object of class "numeric" containing the flow positions for  each base in the called sequence, i.e. for each base, the position in the flowgram whose
flowIndexes：Object类的"numeric"包含在所谓的顺序为每个碱基的流的位置，即每个碱基，在flowgram的位置，其




quality: Object of class "BString" containing the quality scores for each of the bases in the sequence, where
quality：Object类的"BString"包含序列中的每个碱基的质量分数，


方法----------Methods----------




read<- signature(object = "SFFRead", value = "DNAString"):
读< - signature(object = "SFFRead", value = "DNAString")：




read signature(object = "SFFRead"):
读signature(object = "SFFRead")：




flowChars<- signature(object = "SFFContainer", value = "character"):
flowChars < - signature(object = "SFFContainer", value = "character")：




flowChars signature(object = "SFFContainer"):
flowCharssignature(object = "SFFContainer")：




flowgramFormat<- signature(object = "SFFContainer", value = "numeric"):
flowgramFormat < - signature(object = "SFFContainer", value = "numeric")：




flowgramFormat signature(object = "SFFContainer"):
flowgramFormatsignature(object = "SFFContainer")：




keySequence<- signature(object = "SFFContainer", value = "character"):
keySequence < - signature(object = "SFFContainer", value = "character")：




keySequence signature(object = "SFFContainer"):
keySequencesignature(object = "SFFContainer")：




clipAdapterLeft<- signature(object = "SFFRead", value = "numeric"):
clipAdapterLeft < - signature(object = "SFFRead", value = "numeric")：




clipAdapterLeft signature(object = "SFFRead"):
clipAdapterLeftsignature(object = "SFFRead")：




clipAdapterRight<- signature(object = "SFFRead", value = "numeric"):
clipAdapterRight < - signature(object = "SFFRead", value = "numeric")：




clipAdapterRight signature(object = "SFFRead"):
clipAdapterRightsignature(object = "SFFRead")：




clipQualityLeft<- signature(object = "SFFRead", value = "numeric"):
clipQualityLeft < - signature(object = "SFFRead", value = "numeric")：




clipQualityLeft signature(object = "SFFRead"):
clipQualityLeftsignature(object = "SFFRead")：




clipQualityRight<- signature(object = "SFFRead", value = "numeric"):
clipQualityRight < - signature(object = "SFFRead", value = "numeric")：




clipQualityRight signature(object = "SFFRead"):
clipQualityRightsignature(object = "SFFRead")：




flowgram<- signature(object = "SFFRead", value = "numeric"):
flowgram < - signature(object = "SFFRead", value = "numeric")：




flowgram signature(object = "SFFRead"):
flowgramsignature(object = "SFFRead")：




flowIndexes<- signature(object = "SFFRead", value = "numeric"):
flowIndexes < - signature(object = "SFFRead", value = "numeric")：




flowIndexes signature(object = "SFFRead"):
flowIndexessignature(object = "SFFRead")：




name<- signature(object = "SFFRead", value = "character"):
名< - signature(object = "SFFRead", value = "character")：




name signature(object = "SFFRead"):
名称signature(object = "SFFRead")：




quality<- signature(object = "SFFRead", value = "BString"):
质量< - signature(object = "SFFRead", value = "BString")：




quality signature(object = "SFFRead"):
质量signature(object = "SFFRead")：


作者（S）----------Author(s)----------



Christian Ruckert




参见----------See Also----------

readSFF, SFFContainer
readSFF，SFFContainer


举例----------Examples----------


showClass("SFFRead")

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


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