snp.dprime-class(chopsticks)
snp.dprime-class()所属R语言包：chopsticks
Class "snp.dprime" for Results of LD calculation
类的“snp.dprime”劳工处的计算结果
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The snp.dprime class encapsulates results returned by ld.snp (— routine to calculate D', $r^2$ and LOD of a snp.matrix-class object, given a range and a depth) and is based on a list of three named matrices.
snp.dprime类封装ld.snp返回的结果（ - 常规计算D“，$ R ^ 2 $和LOD的snp.matrix-class对象，范围和深度）基于三个名为矩阵的列表。
The lower right triangle of the snp.dprime object returned by ld.snp always consists zeros. This is delibrate. The associated plotting routine would not normally access those elements either.
ld.snp总是由零较低直角三角形的snp.dprime对象返回。这是研讨。相关的绘图程序将无法正常访问这些元素。
值----------Value----------
The snp.dprime class is a list of 3 named matrices dprime, rsq2 or r, lod, and an attribute snp.names for the list of snps involved. (Note that if $x$ snps are involved, the row numbers of the 3 matrices are $(x-1)$). Only one of r or rsq2 is present.
类snp.dprime 3名为矩阵列表dprime，rsq2或r，lod，属性snp.names名单单核苷酸多态性参与。 （请注意，如果$ X $ SNPs是参与，3个矩阵的行数分别为（X-1）$）。只有一个r或rsq2存在。
参数：dprime
D'
D“
参数：rsq2
$r^2$
$ R ^ 2元
参数：r
signed $r^2$
签署$ R ^ 2 $
参数：lod
Log of Odd's
登录奇
参数：attr(*, class)
"snp.dprime"
“snp.dprime”
参数：attr(*, snp.names)
character vectors of the snp names involved
SNP涉及名称的特征向量
All the matrices are defined such that the ($n, m$)th entry is the pair-wise value between the ($n$)th snp and the $(n+m)$th snp. Hence the lower right triangles are always filled with zeros.
美元（N + M）$个SNP（N，M $），次入口是成对的值（$ N $）个SNP和所有的矩阵定义等。因此，在右下角的三角形总是用零填充。
Invalid values are represented by an out-of-range value - currently we use -1 for D', $r^2$ (both of which are between 0 and 1), and -2 for $r$ (valid values are between -1 and +1). lod is set to zero in most of these invalid cases. (lod can be any value so it is not indicative).
无效的值表示范围的价值 - 目前我们使用D“-1，$ R ^ 2元（其中0和1之间），$ R $ -2（有效值介于-1和+1）。 LOD设置在大多数这些无效的情况下为零。 （LOD可以是任何值，所以它是不指示）。
方法----------Methods----------
See plot.snp.dprime.
看到plot.snp.dprime。
注意----------Note----------
TODO: Need a subsetting operator.
TODO：需要一个子集运算符。
TODO: an assemble operator
TODO：在组装操作员
作者（S）----------Author(s)----------
Hin-Tak Leung <a href="mailto:htl10@users.sourceforge.net">htl10@users.sourceforge.net</a>
源----------Source----------
~~ reference to a publication or URL from which the data were obtained ~~
~参考出版物或网址，从该数据获得了~~
参考文献----------References----------
举例----------Examples----------
data(testdata)
snps20.20 <- Autosomes[11:20,11:20]
obj.snp.dprime <- ld.snp(snps20.20)
class(obj.snp.dprime)
summary(obj.snp.dprime)
## Not run: [＃无法运行：]
# The following isn't executable-as-is example, so these illustrations[以下是不是可执行文件作为例子，所以这些插图]
# are commented out to stop R CMD check from complaining:[被注释掉停止抱怨R CMD检查：]
> d<- ld.snp(all, 3, 10, 15)
rows = 48, cols = 132
... Done
> d
$dprime
[,1] [,2] [,3]
[1,] 1 1 1
[2,] 1 1 1
[3,] 1 1 1
[4,] 1 1 0
[5,] 1 0 0
$rsq2
[,1] [,2] [,3]
[1,] 1.0000000 0.9323467 1.0000000
[2,] 0.9285714 1.0000000 0.1540670
[3,] 0.9357278 0.1854481 0.9357278
[4,] 0.1694915 1.0000000 0.0000000
[5,] 0.1694915 0.0000000 0.0000000
$lod
[,1] [,2] [,3]
[1,] 16.793677 11.909686 16.407120
[2,] 10.625650 15.117962 2.042668
[3,] 12.589586 2.144780 12.589586
[4,] 2.706318 16.781859 0.000000
[5,] 2.706318 0.000000 0.000000
attr(,"class")
[1] "snp.dprime"
attr(,"snp.names")
[1] "dil118" "dil119" "dil5904" "dil121" "dil5905" "dil5906"
## End(Not run)[＃结束（不运行）]
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 15:01:17
