filterMicroRna(AgiMicroRna)
filterMicroRna()所属R语言包：AgiMicroRna
Filtering Genes
筛选基因
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Filter genes out according to their Quality Flag
根据其质量标志的筛选基因
用法----------Usage----------
filterMicroRna(ddNORM,
dd,
control,
IsGeneDetected,
wellaboveNEG,
limIsGeneDetected,
limNEG,
makePLOT,
targets,
verbose,
writeout)
参数----------Arguments----------
参数：ddNORM
uRNAList with the Total Gene Signal in log2 scale to be FILTERED out according to a Quality FLAG
以log2规模的共有基因信号被过滤掉uRNAList根据质量标志
参数：dd
uRNAList, containing the output from readMicroRnaAFE
uRNAList，包含从readMicroRnaAFE输出
参数：control
logical, if TRUE it removes controls
逻辑控制，如果TRUE它删除
参数：IsGeneDetected
logical, if TRUE it filters genes according to gIsGeneDetected Flag. Flag = 1, then gene is detected
逻辑，如果TRUE筛选基因gIsGeneDetected旗。标志= 1，那么基因检测
参数：wellaboveNEG
logical, if TRUE it filter genes whose expression is not above a limit value defined by the expression of negative controls. Limit= Mean(negative) + 1.5 x sd(negative)
逻辑，如果TRUE过滤基因的表达是不高于表达阴性对照定义的限值。限额=平均（负）+ 1.5×SD（负）
参数：limIsGeneDetected
for a given feature xi accros samples, is the minimum in at least one experimental condition with a IsGeneDetected-FLAG = 1 (Is Detected)
对于一个给定的功能第十一accros样品，至少在一个实验条件与IsGeneDetected旗最低= 1（检测）
参数：limNEG
for a given feature xi accros samples, is the minimum in at least one experimental condition with intensity > Limit established for negative controls (Mean + 1.5 x SD)
对于一个给定的功能第十一accros样品，至少是在实验条件下至少有一个强度>限额为阴性对照组（平均+ 1.5×SD）
参数：makePLOT
logical, if TRUE makes QC plots with the remaining signals
逻辑，如果TRUE使得其余信号的质量控制图
参数：targets
data.frame with the targets structure
数据框与目标结构
参数：verbose
logical, if TRUE prints out output
逻辑，如果TRUE打印出输出
参数：writeout
logical, if TRUE writes out output files
逻辑，如果TRUE写输出文件
Details
详情----------Details----------
Agilent Feature Extraction software provides a flag for each spot that identifies different quantification errors of the signal. Quantification flags were used to filter out signals that did not reach a minimum established criterion of quality.
安捷伦特征提取软件提供了一个为每个点确定了不同的量化误差信号旗。量化标志被用来筛选出的信号，没有达到最低标准建立的质量。
值----------Value----------
The function returns a uRNAList containing the FILTERED data. In order to allow the tracking of those microRNAs that may have been filtered out from the original raw data, the following files are given:
该函数返回一个包含过滤数据的uRNAList。为了让跟踪那些可能已经从原始数据过滤的小分子RNA，下列文件：
NOCtrl\_exprs.txt: Log2 Normalized Total Gene Signals for the Non Control Genes NOCtrl\_FlagIsGeneDetected.txt: IsGeneDetected Flag for the Non Control Genes, 1 = detected IsNOTGeneDetected.txt: Genes that not are not detected according to IsGeneDetected Flag
NOCtrl \ _exprs.txt：Log2归为共有的基因信号控制基因NOCtrl \ _FlagIsGeneDetected.txt：IsGeneDetected国旗控制基因，1 = IsNOTGeneDetected.txt：基因检测未检出根据IsGeneDetected旗
作者（S）----------Author(s)----------
Pedro Lopez-Romero
参考文献----------References----------
http://www.Agilent.com
举例----------Examples----------
data(dd.micro,verbose=FALSE)
data(targets.micro,verbose=FALSE)
ddTGS=tgsMicroRna(dd.micro,half=TRUE,makePLOT=FALSE,verbose=FALSE)
ddNORM=tgsNormalization(ddTGS,'quantile',
makePLOTpre=FALSE,makePLOTpost=TRUE,targets.micro,verbose=FALSE)
ddPROC=filterMicroRna(ddNORM,
dd.micro,
control=TRUE,
IsGeneDetected=TRUE,
wellaboveNEG=FALSE,
limIsGeneDetected=50,
limNEG=25,
makePLOT=FALSE,
targets.micro,
verbose=FALSE,
writeout=FALSE)
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 11:38:18
