dba.peakset(DiffBind)
dba.peakset()所属R语言包：DiffBind
Add a peakset to, or retrieve a peakset from, a DBA object
添加peakset到，或检索从一个DBA对象peakset
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Adds a peakset to, or retrieves a peakset from, a DBA object
增加了一个peakset到，或检索从一个DBA对象1 peakset
用法----------Usage----------
dba.peakset(DBA=NULL, peaks, sampID, tissue, factor, condition, replicate,
control, peak.caller, reads=0, consensus=FALSE,
bamReads, bamControl,
normCol=4, bRemoveM=TRUE, bRemoveRandom=TRUE,
minOverlap=2, bMerge=TRUE,
bRetrieve=FALSE, writeFile, numCols=4,
bRangedData=DBA$config$RangedData)
参数----------Arguments----------
参数：DBA
DBA object. Required unless creating a new DBA object by adding an initial peakset.
DBA的对象。必需的，除非通过添加一个初始peakset创建一个新的DBA对象。
参数：peaks
When adding a specified peakset: set of peaks, either a RangedData object, a peak matrix (chr,start,end,score), or a filename where the peaks are stored. When adding a consensus peakset: a sample mask or vector of peakset numbers. If missing or NULL, a consensus is derived from all peaksets present in the model. See dba.mask, or dba.show to get peakset numbers. When adding all the peaks from one DBA object to another: a DBA object. In this case, the only other parameter to have an effect is minOverlap. When retrieving and/or writing a peakset: a peak matrix or RangedData object, or a peakset number; if NULL, retrieves/writes the full binding matrix.
当加入一个指定peakset：设置峰，无论是RangedData对象，高峰矩阵（CHR，开始，结束时，分），或峰存储的文件名。加入共识peakset时：样本面罩或peakset数的向量。如果遗失或NULL，一个共识是来自模型中存在的所有peaksets。参见，dba.mask，或dba.show得到peakset数。当从一个DBA对象到另一个高峰：一个DBA对象。在这种情况下，唯一有效果的其他参数是minOverlap。当检索和/或写peakset：峰值矩阵或RangedData对象，或peakset数量，如果为NULL，检索/写完整的结合矩阵。
参数：sampID
ID string for the peakset being added; if missing, one is assigned (a serial number for a new peakset, or a concatenation of IDs for a consensus peakset).
ID为peakset字符串被添加;如果缺少，一个是分配给（序号为一个新的peakset，或串联的ID共识peakset）。
参数：tissue
tissue name for the peakset being added; if missing, one is assigned for a consensus peakset (a concatenation of tissues).
组织名称为peakset;如果缺少，一个是为共识peakset分配（组织串联）。
参数：factor
factor name for the peakset being added; if missing, one is assigned for a consensus peakset (a concatenation of factors).
因素peakset的名字;如果缺少，一个是为共识peakset分配（串联的因素）。
参数：condition
condition name for the peakset being added; if missing, one is assigned for a consensus peakset (a concatenation of conditions).
条件peakset的名字;如果缺少，一个是为共识peakset分配（条件的串联）。
参数：replicate
replicate number for the peakset being added; if missing, one is assigned for a consensus peakset (a concatenation of replicate numbers).
复制添加peakset号;如果缺少，一个是为的共识peakset（串联重复号码）分配。
参数：control
control name for the peakset being added; if missing, one is assigned for a consensus peakset (a concatenation of control names).
控制添加peakset的名称;如果缺少，一个是分配为的共识peakset（控制名称的串联）。
参数：peak.caller
peak caller name string. If peaks is specified as a file, this will control how it is interpreted. Supported values:
高峰来电者姓名的字符串。如果峰被指定为一个文件，这将解释它是如何控制。支持的值：
“raw”: text file file; peak score is in fourth column
“原始”：文本文件;高峰的得分是在第四列
“bed”: .bed file; peak score is in fifth column
“床”：床文件;高峰得分在第五纵队。
“macs”: MACS .xls file
“互委会”：磁珠xls文件。
“swembl”: SWEMBL .peaks file
“swembl”：SWEMBL峰文件
“bayes”: bayesPeak file
“贝斯”：bayesPeak文件
“peakset”: peakset written out using pv.writepeakset
“peakset”：书面peakset出使用pv.writepeakset
“fp4”: FindPeaks v4
“FP4”：FindPeaks V4
if missing, a name is assigned for a consensus peakset (a concatenation of peak caller names).
如果缺少，分配一个名称为的共识peakset（高峰主叫姓名的串联）。
参数：reads
total number of ChIPed library reads for the peakset being added.
总数ChIPed库读取添加peakset。
参数：consensus
TRUE if peakset being added is made from overlap of other peaksets (set automatically when adding a consensus peakset).
TRUE，如果添加peakset，从其他peaksets（设置自动加入共识peakset时）重叠。
参数：bamReads
file path of the BAM/SAM/BED file containing the aligned reads for the peakset being added.
BAM / SAM /床含对齐的文件的文件路径读取添加peakset。
参数：bamControl
file path of the BAM/SAM/BED file containing the aligned reads for the control used for the peakset being added.
BAM / SAM /床含对齐的文件的文件路径读取为用于添加peakset的控制。
参数：normCol
peak column to normalize to 0...1 scale when adding a peakset; 0 indicates no normalization
峰列标准化0 ... 1规模增加1 peakset时，0表示没有标准化
参数：bRemoveM
logical indicating whether to remove peaks on chrM when adding a peakset
逻辑指示是否删除特征剩磁峰增加1 peakset时
参数：bRemoveRandom
logical indicating whether to remove peaks on chrN_random when adding a peakset
逻辑表明是否峰上chrN_random删除增加1 peakset时
参数：minOverlap
the minimum number of peaksets a peak must be in to be included when adding a consensus peakset.
最低peaksets高峰必须要包括加入共识peakset时。
参数：bMerge
logical indicating whether global binding matrix should be compiled after adding the peakset. When adding several peaksets via successive calls to dba.peakset, it may be more efficient to set this parameter to FALSE and call dba(DBA) after all the peaksets have been added.
逻辑表明是否有全球约束力的矩阵应添加的peakset后的编译。当添加通过连续dba.peakset呼叫几个peaksets，它可能是更有效，毕竟peaksets已加入到将此参数设置为FALSE，并且调用DBA（DBA）。
参数：bRetrieve
logical indicating that a peakset is being retrieved and/or written, not added.
逻辑表明，peakset被检索和/或书面，不添加。
参数：writeFile
file to write retrieved peakset.
文件写检索peakset。
参数：numCols
number of columns to include when writing out peakset. First four columns are chr, start, end, score; the remainder are maintained from the original peakset. Ignored when writing out complete binding matrix.
列包括写出来peakset时。前4列是字符，起点，终点，成绩;其余维持从原来peakset的。写出完整的结合矩阵时忽略。
参数：bRangedData
logical indicating whether, if bRetrieve is TRUE, the peakset should be returned as a RangedData object. Can be set as default behavior by setting DBA$config$RangedData=TRUE.
逻辑表明，是否如果bRetrieve为TRUE，在peakset应作为RangedData对象返回。设置DBA的美元配置$ RangedData = TRUE，可以设置为默认的行为。
Details
详情----------Details----------
MODE: Add a specified peakset:
模式：添加指定peakset：
dba.peakset(DBA=NULL, peaks, sampID, tissue, factor, condition, replicate, control, peak.caller, reads, consensus, bamReads, bamControl, normCol, bRemoveM, bRemoveRandom)
dba.peakset（DBA = NULL，则峰，sampID，组织因素，条件，复制，控制，peak.caller，读，达成共识，bamReads，bamControl，normCol，bRemoveM，bRemoveRandom）
MODE: Add a consensus peakset (derived from overlapping peaks in peaksets already present):
模式：添加的共识peakset（目前在peaksets已经从重叠峰的）：
dba.peakset(DBA, peaks, minOverlap)
dba.peakset（DBA的山峰，minOverlap）
MODE: Retrieve a peakset:
模式：检索peakset：
dba.peakset(DBA, peaks, bRetrieve=T)
dba.peakset（DBA，山峰，bRetrieve = T）
MODE: Write a peakset out to a file:
模式：写peakset到一个文件：
dba.peakset(DBA, peaks, bRetrieve=T, writeFile, numCols)
dba.peakset（DBA的山峰，bRetrieve = T，WriteFile的，NUMCOLS）
值----------Value----------
DBA object when adding a peakset. Peakset matrix or RangedData object when retrieving and/or writing a peakset.
DBA的对象时加入一个peakset。 peakset矩阵或RangedData的对象时，检索和/或写peakset。
作者（S）----------Author(s)----------
Rory Stark
举例----------Examples----------
# create a new DBA object by adding three peaksets[添加三个peaksets创建一个新的DBA对象]
mcf7 = dba.peakset(NULL,
peaks=system.file("extra/peaks/MCF7_ER_1.bed.gz", package="DiffBind"),
sampID="MCF7.1",tissue="MCF7",factor="ER",condition="Responsive",replicate=1)
mcf7 = dba.peakset(mcf7,
peaks=system.file("extra/peaks/MCF7_ER_2.bed.gz", package="DiffBind"),
sampID="MCF7.2",tissue="MCF7",factor="ER",condition="Responsive",replicate=2)
mcf7 = dba.peakset(mcf7,
peaks=system.file("extra/peaks/MCF7_ER_3.bed.gz", package="DiffBind"),
sampID="MCF7.3",tissue="MCF7",factor="ER",condition="Responsive",replicate=3)
mcf7
#add a consensus peakset -- peaks in all three replicates[添加的共识peakset - 在所有三个峰复制]
mcf7 = dba.peakset(mcf7, 1:3, minOverlap=3,sampID="MCF7_3of3")
mcf7
#retrieve the consensus peakset as RangedData object[检索RangedData对象的共识peakset]
mcf7.consensus = dba.peakset(mcf7,mcf7$masks$Consensus,bRetrieve=TRUE)
mcf7.consensus
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 16:39:28
