cisProxScores(GGtools)
cisProxScores()所属R语言包：GGtools
create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions
创建结合起来，和收获eqtlTestsManager实例收集所有满足eQTL测试某些基因接近条件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
create, combine, and harvest eqtlTestsManager instances to collect all eQTL tests satisfying certain gene proximity conditions
创建结合起来，和收获eqtlTestsManager实例收集所有满足eQTL测试某些基因接近条件
用法----------Usage----------
cisProxScores(smlSet, fmla, dradset, direc = NULL, folder, runname, geneApply = lapply, saveDirector = TRUE, snpGRL=NULL,
geneGRL=NULL, snpannopack="SNPlocs.Hsapiens.dbSNP.20100427", ffind=NULL, ...)
#mcisProxScores (listOfSmlSets, listOfFmlas, dradset, direc = NULL,
# folder, runname, geneApply = lapply, saveDirector = TRUE,
# makeCommonSNPs = FALSE, snpGRL=NULL,
# geneGRL=NULL, snpannopack="SNPlocs.Hsapiens.dbSNP.20100427", ffind=NULL, ...)
#
interleave2cis( cisp, permcisp )
scoresByGenes(cps, intvind = 1, as.GRanges=TRUE, dups2max=TRUE, snpGR=NULL,
scoreConverter=function(x)x )
参数----------Arguments----------
参数：smlSet
instance of smlSet-class
实例smlSet-class
参数：fmla
the right-hand side of a standard modeling formula – no dependent variable; the expression values in the smlSet will be used successively as dependent variables
标准建模公式右边 - 没有因变量;在smlSet“表达式的值将被用来先后为因变量
参数：dradset
a numeric vector indicating the boundaries within which test scores will be tabulated. For example, if dradset is c(5000,10000,25000) then scores will be tabulated for SNP in the regions (0-5kb) from start or end of gene, (5-10kb), (10-25kb).
数字矢量显示考试成绩将表内的边界。例如，如果dradset是c(5000,10000,25000)然后成绩将表列的SNP（0-5KB）在该区域，从基因的开始或结束（5-10KB），（10-25KB）。
参数：direc
an instance of multiCisDirector-class; if non-null, eqtlTests will not be run, but the tests managed by managers in the direc instance will be used
一个实例multiCisDirector-class;如果非空，eqtlTests将不能运行，但经理管理direc测试实例将被用来
参数：folder
used to set targdir parameter when eqtlTests is run; ignored if direc is non-null
使用设置targdir参数“时eqtlTests运行;忽略direc如果非空
参数：runname
used to set runname parameter when eqtlTests is run; some mangling will be applied. Ignored if direc is non-null
用于设置runname时eqtlTests运行的参数;将应用于一些重整。忽略direc如果非空
参数：geneApply
iteration function (like lapply) to be used for each expression probe (gene); passed to eqtlTests; the setting is also used for some annotation-based iterations; if multicore package is present, setting this parameter to mclapply is advised
迭代函数（如lapply）用于每个表达式的探针（基因）传递到eqtlTests设置也用于一些基于注解的迭代，如果多核包存在，将此参数设置mclapply建议
参数：saveDirector
logical; since it is expensive to compute the multiCisDirector that will be harvested, we may want to serialize it; if so set saveDirector to TRUE. If set to true the function stores an object with name paste(folder,"_director",".rda",sep="") in the current working folder.
逻辑，因为它是昂贵的计算将收获multiCisDirector，我们可能要序列化;若有设置saveDirector为TRUE。如果设置为true的功能存储对象的姓名paste(folder,"_director",".rda",sep="")在当前的工作文件夹。
参数：...
arguments passed to eqtlTests
参数传递eqtlTests
参数：listOfSmlSets
for mcisProxScores, a list of smlSets that are to be sources for eQTL test scores that will be summed
，mcisProxScores eQTL测试将总结成绩的来源smlSets列表
参数：listOfFmlas
for mcisProxScores, a list of formulas to be used with snp.rhs.tests, assumed to be ordered to correspond to elements of listOfSmlSets
mcisProxScores，snp.rhs.tests，假定责令对应元素listOfSmlSets公式列表
参数：makeCommonSNPs
for mcisProxScores, a logical telling whether the sets of SNPs elements of the listOfSmlSets should be reduced to their intersection; this can be slow, and can be done externally using the function of the same name.
mcisProxScores，逻辑告诉套listOfSmlSets单核苷酸多态性元素是否应减少它们的交集，这可能会很慢，可以做外部使用的名称相同的功能。
参数：snpGRL
named list of GRanges instances with SNP locations; list element names must coincide with names of smList entries in smlSet
SNP的位置名为农庄实例列表，列表元素名称必须一致smList条目名称在smlSet
参数：geneGRL
named list of GRanges instances with gene extents; list element names must coincide with names of smList entries in smlSet
基因扩展的名为农庄实例列表，列表元素名称必须一致smList条目名称在smlSet
参数：snpannopack
string naming package with SNPlocs information
SNPlocs信息字符串命名包
参数：cisp
result of cisProxScores
导致cisProxScores
参数：permcisp
result of cisProxScores
导致cisProxScores
参数：ffind
usually 1 for cis applications where one chromosome of SNP is selected at a time
通常1顺一次选择其中一个染色体的SNP的应用
参数：cps
instance of cisProxScores-class
实例cisProxScores-class
参数：intvind
index of cis interval to be evaluated (usually the cisProxScores has been run with a dradset specifying a set of disjoint intervals, given by names(cps), for example, where cps is the cisProxScores instance
独联体间隔的指标进行评价（通常的cisProxScores已运行dradset指定一组不相交的区间，由名称（郊野公园段），例如，在CPS是cisProxScores的实例
参数：as.GRanges
logical indicating that scores should be returned bound to GRanges for SNP addresses
逻辑说明，分数应退还的SNP地址绑定到农庄
参数：dups2max
logical indicating policy for dealing with SNP that occur multiple times in this gene-oriented survey – the duplicate SNP are reduced to the highest-scoring one
逻辑处理与SNP发生在该基因为导向的调查多次表明的政策 - 重复SNP降低到最高得分
参数：snpGR
GRanges instance with SNP addresses – need not be identical to set of SNP analyzed
农庄与SNP地址的实例 - 需要不相同设置的SNP分析
参数：scoreConverter
a function accepting and returning numeric; for minus log10 p, use scoreConverter=function(x)-log10(1-pchisq(x,df)), where df is typically 1
接受和返回数字的功能;为零下LOG10带够，使用scoreConverter=function(x)-log10(1-pchisq(x,df))，其中DF通常为1
Details
详情----------Details----------
This function computes tests for all same-chromosome eQTL up to the maximum distance given in dradset and returns a named list with chi-squared statistics computed by snp.rhs.tests
此函数计算所有相同的染色体eQTL测试的最大距离在dradset返回一个snp.rhs.tests计算卡方统计列表命名为
The interleave2cis function helps with general comparison of distributions of real scores to distributions obtained after permutation of expression values against genotypes. See the example.
interleave2cis功能有助于以表达对基因型值的排列后得到的分布与真实分数的分布一般比较。见的例子。
值----------Value----------
a list with one component per "radius" derived from dradset
与“方圆”的每一个组成部分的列表，从dradset派生
each radius-associated component includes a list with one element per chromosome of the SNP data in the smlSet
每个半径相关的组件，包括与每一个染色体的SNP数据元素列表smlSet
each chromosome-associated sublist includes a list for each gene mapped to the chromosome, with contents a column-vector of test results for all SNP within the radius of the enclosing component; see the example for further concreteness
每个染色体相关的子表包括一个映射到染色体上，与内容的封闭组件的半径范围内的所有SNP的检测结果列向量，每个基因的列表;看到进一步具体的例子
作者（S）----------Author(s)----------
VJ Carey <stvjc@channing.harvard.edu>
参见----------See Also----------
eqtlTests
eqtlTests
举例----------Examples----------
## Not run: [＃无法运行：]
if (!exists("hmceuB36.2021")) hmceuB36.2021 <- getSS("GGtools", c("20", "21"))
hm = hmceuB36.2021
td = tempdir()
cd = getwd()
on.exit(setwd(cd))
setwd(td)
library(illuminaHumanv1.db)
g20 = intersect(get("20", revmap(illuminaHumanv1CHR)),
featureNames(hm))[1:10]
g21 = intersect(get("21", revmap(illuminaHumanv1CHR)),
featureNames(hm))[1:10]
hm = hm[probeId(c(g20,g21)), ] # restrict to small number of genes[限制少数基因]
try(unlink("man", recursive=TRUE)) # in tempdir[在TEMPDIR]
set.seed(1234) # necessary for dealing with null imputation of missing[必要的处理空归集与失踪]
f1 = cisProxScores( hm, ~male, c(5000,10000,25000), folder="man",
runname="man", geneApply=lapply, ffind=1 )
length(f1) # number of proximity regions specified in dradset[在dradset指定的邻近区域的数]
length(f1[[1]]) # number of chromosomes of SNP data in smlSet[数染色体的SNP数据在smlSet]
length(f1[[1]][[1]]) # number of genes in smlSet[smlSet基因数]
# mapping to first chromosome in smlSet [映射到第一号染色体中smlSet]
# SNP data[SNP数据]
length(f1[[1]][[2]]) # number of genes mapping to second chr...[映射到第二个字符的基因数目...]
sapply(f1, function(x)max(unlist(x)))
sapply(f1, function(x)length(x[[1]]))
lapply(f1, function(x)names(x[[1]]))
lapply(f1, function(x)rownames(x[[1]][[1]][[1]]))
set.seed(1234)
try(unlink("pman", recursive=TRUE)) # in tempdir[在TEMPDIR]
pf1 = cisProxScores( permEx(hm), ~male, c(5000, 10000, 25000), folder="pman",
runname="pman", geneApply=lapply, ffind=1)
i1o = interleave2cis( f1, pf1 )
opar = par(no.readonly=TRUE)
par(las=2, mar=c(12, 5, 5, 5))
boxplot(lapply(i1o, unlist), range=0, main="compare observed to expr-permuted eQTL test scores")
par(opar)
load("man_director.rda")
man_director
setwd(cd)
## End(Not run)[＃结束（不运行）]
## Not run: [＃无法运行：]
cd = getwd()
td = tempdir()
on.exit(setwd(cd))
set.seed(1234) # necessary for dealing with null imputation of missing[必要的处理空归集与失踪]
mm = mcisProxScores( list(hm,hm), list(~male,~male),
dradset=c(5000,10000,25000), folder="mmm", runname="MMM", ffind=1)
setwd(cd)
## End(Not run)[＃结束（不运行）]
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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 19:45:49
