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

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

                                        Class "SFFContainer"
                                         类“SFFContainer”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is a container for data from files in Roche's Standard Flowgram Format (SFF).
这个类是一个数据从罗氏的标准Flowgram的格式（SFF）中的文件的容器。


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

Objects can be created by calls of the form new("SFFContainer", ...). Usually, objects will be created by calling the readSFF method on a file in SFF  format.
创建对象可以通过检测的形式new("SFFContainer", ...)。通常，对象将被创建调用readSFF方法上的SFF格式的文件。


插槽----------Slots----------




name: Object of class "character" containing the name of the file this
name类"character"包含的文件名：对象




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 for each read. If only a  combined (quality+adapter) clipping position is computed it should be stored in  clipQualityLeft. If no clipping value is computed the field is set to 0. The position values
clipQualityLeft：Object类的"numeric"代表每次读取的附加质量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。如果没有裁剪值计算字段设置为0。位置值




clipQualityRight: Object of class "numeric" representing the position of  the last base before the clipping point for an attached quality sequence for each read. If  only a combined (quality+adapter) clipping position is computed it should be stored in  clipQualityRight. If no clipping value is computed the field is set to 0. The position values
clipQualityRight：Object类的"numeric"代表每次读取的附加质量序列的最后一个碱基的剪裁点前的位置。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityRight。如果没有裁剪值计算字段设置为0。位置值




clipAdapterLeft: Object of class "numeric" representing the position of the  first base after the clipping point for an attached adapter sequence for each read. If only a  combined (quality+adapter) clipping position is computed it should be stored in  clipQualityLeft. If no clipping value is computed the field is set to 0. The position values
clipAdapterLeft：Object类的"numeric"代表读每个连接的适配器顺序的剪辑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。如果没有裁剪值计算字段设置为0。位置值




clipAdapterRight: Object of class "numeric" representing the position of  the last base before the clipping point for an attached adapter sequence for each read. If  only a combined (quality+adapter) clipping position is computed it should be stored in  clipQualityRight. If no clipping value is computed the field is set to 0. The position values
clipAdapterRight：Object类的"numeric"代表一个附加适配器每个读序列的最后一个碱基的剪裁点前的位置。如果只计算合并（质量+适配器）裁剪位置，它应存放在clipQualityRight。如果没有裁剪值计算字段设置为0。位置值




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




flowIndexes: Object of class "list" 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"list"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




reads: Object of class "QualityScaledDNAStringSet" containing the  basecalled nucleotide sequences of each read together with the quality scores for each of the
reads：类对象"QualityScaledDNAStringSet"包含每个basecalled核苷酸序列一起阅读的质量分数


方法----------Methods----------




addRead signature(object = "SFFContainer", read = "SFFRead"): Adds an object of
addReadsignature(object = "SFFContainer", read = "SFFRead")：添加对象




getRead signature(object = "SFFContainer", readname = "character"): Returns the
getReadsignature(object = "SFFContainer", readname = "character")：返回




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




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




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




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




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




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




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




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




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




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




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")：




flowgrams<- signature(object = "SFFContainer", value = "list"):
flowgrams < - signature(object = "SFFContainer", value = "list")：




flowgrams signature(object = "SFFContainer"):
flowgramssignature(object = "SFFContainer")：




flowIndexes<- signature(object = "SFFContainer", value = "list"):
flowIndexes < - signature(object = "SFFContainer", value = "list")：




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




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




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




reads<- signature(object = "SFFContainer", value = "QualityScaledDNAStringSet"):
读< - signature(object = "SFFContainer", value = "QualityScaledDNAStringSet")：




reads signature(object = "SFFContainer"):
读取signature(object = "SFFContainer")：




[ signature(x = "SFFContainer", i = "ANY", j = "ANY"):
[signature(x = "SFFContainer", i = "ANY", j = "ANY")：


作者（S）----------Author(s)----------



Christian Ruckert




参见----------See Also----------

readSFF, SFFRead
readSFF，SFFRead


举例----------Examples----------


  showClass("SFFContainer")

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


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