ReadCounts-class(ChIPseqR)
ReadCounts-class()所属R语言包：ChIPseqR
Class "ReadCounts"
类“ReadCounts”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Represents counts of (possibly extended) reads for each strand of the genome.
代表（可能延长）读取每个链的基因组的计数。
用法----------Usage----------
ReadCounts(counts=list(), names=NULL, compress=TRUE)
参数----------Arguments----------
参数：counts
A list of read counts. Each component is a two column matrix of strand specific read counts for a chromosome.
读取计数。每个组件是一个两列的矩阵链的具体读染色体计数。
参数：names
Character vector of chromosome names. If this is NULL the names of counts are used instead.
特征向量染色体的名称。如果这是NULLcounts名称是用来代替。
参数：compress
Logical indicating whether read counts should be compressed.
逻辑表示是否应该压缩读计数。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form ReadCounts(counts, names, compress=FALSE) or by calls to strandPileup.
可以创建形式ReadCounts(counts, names, compress=FALSE)或strandPileup检测的通话对象。
插槽----------Slots----------
counts: Object of class "list" with one component per chromosome, containing a matrix of read counts (one column per strand).
counts：Object类的"list"每一个染色体的组成部分，包含读取计数的矩阵，每串（一列）。
方法----------Methods----------
[<- signature(x = "ReadCounts", i = "ANY", j = "missing"): Replace read counts for chromosomes indicated by i.
[< - signature(x = "ReadCounts", i = "ANY", j = "missing")：替换读取i表示染色体计数。
[ signature(x = "ReadCounts", i = "ANY", j = "missing", drop = "missing"): Returns list of read counts for chromosomes indicated by i.
[signature(x = "ReadCounts", i = "ANY", j = "missing", drop = "missing")：i返回列表读取计数染色体的表示。
[[<- signature(x = "ReadCounts", i = "ANY", j = "missing"): Replace read counts for chromosome i.
[< - signature(x = "ReadCounts", i = "ANY", j = "missing")：替换为染色体i读取计数。
[[ signature(x = "ReadCounts", i = "ANY", j = "missing"): Returns read counts for chromosome i.
[signature(x = "ReadCounts", i = "ANY", j = "missing")：返回阅读染色体i的罪名。
$<- signature(x = "ReadCounts"): Replace read counts for chromosome i (by name).
$ < - signature(x = "ReadCounts")：的染色体i（姓名），更换阅读计数。
$ signature(x = "ReadCounts"): Returns read counts for chromosome i (by name).
$signature(x = "ReadCounts")：返回为染色体i（名称）读取计数。
callBindingSites signature(data = "ReadCounts"): Predict bindingsites from read counts.
callBindingSitessignature(data = "ReadCounts")：预测从只读计数bindingsites。
chrLength signature(x = "ReadCounts", subset = "ANY"): Returns length of all chromosomes represented in x.
chrLengthsignature(x = "ReadCounts", subset = "ANY")：返回长度代表x的所有染色体。
lapply signature(X = "ReadCounts"): Apply function to read counts for each chromosome.
lapplysignature(X = "ReadCounts")：应用函数来读取每条染色体计数。
length<- signature(x = "ReadCounts"): Change the number of chromosomes represented by x to value.
长度< - signature(x = "ReadCounts")：更改xvalue代表染色体的数目。
length signature(x = "ReadCounts"): Number of chromosomes represented by x.
长度signature(x = "ReadCounts")：x代表的染色体数目。
names<- signature(x = "ReadCounts", value = "ANY"): Change names of chromosomes.
名称< - signature(x = "ReadCounts", value = "ANY")：染色体更改名称。
names signature(x = "ReadCounts"): Chromosome names.
名称signature(x = "ReadCounts")：染色体的名字。
nreads signature(x = "ReadCounts", byStrand = "Logical", subset = "ANY"): Returns the number of reads on each chromosome, split by strand (if byStrand is TRUE).
nreadssignature(x = "ReadCounts", byStrand = "Logical", subset = "ANY")：返回读取每条染色体上的数量，由链分裂（byStrand如果是TRUE）。
sapply signature(X = "ReadCounts"): Apply function to read counts for each chromosome.
sapplysignature(X = "ReadCounts")：应用函数来读取每条染色体计数。
作者（S）----------Author(s)----------
Peter Humburg
参见----------See Also----------
BindScore, strandPileup , compress, decompress
BindScore，strandPileup，compress，decompress
举例----------Examples----------
showClass("ReadCounts")
## generate some very simple artificial read data[＃产生一些非常简单的人工读取数据。]
set.seed(1)
fwd <- sample(c(50:70, 250:270), 30, replace=TRUE)
rev <- sample(c(197:217, 347:417), 30, replace=TRUE)
## create data.frame with read positions as input to strandPileup[＃创建一个数据框读输入到strandPileup的位置]
reads <- data.frame(chromosome="chr1", position=c(fwd, rev),
length=25, strand=factor(rep(c("+", "-"), times=c(30, 30))))
## create object of class ReadCounts[＃创建对象类ReadCounts]
readPile <- strandPileup(reads, chrLen=500, extend=1, plot=FALSE, compress=FALSE)
names(readPile)
length(readPile)
sapply(readPile, sum)
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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 14:53:11
