X2chunk(GGtools)
X2chunk()所属R语言包：GGtools
compute numerical matrix of chisq statistics in a genomic interval; extract features as requested
数值计算在基因组区间矩阵chisq统计;提取功能的要求
译者：生物统计家园网 机器人LoveR
描述----------Description----------
compute numerical matrix of chisq statistics in a genomic interval (rows are SNP, columns are genes), or extract features
chisq统计数值矩阵计算在基因组区间（行单核苷酸多态性，列是基因），或提取功能
用法----------Usage----------
X2chunk(mgr, ffind, start, end, snplocs, anno, useSym)
topFeats( x, ... )
# additional potential args include
# mgrOrCTD, ffind, anno, n=10, useSym=TRUE, minMAF=0, minGTF=0 )
参数----------Arguments----------
参数：x
for topFeats, an instance of probeId-class or rsid-class or genesym or eqtlTestsManager classes; this is an API change because of odd logic of old function; to use old behavior, call GGtools:::.topFeats
为topFeats，probeId-class或rsid-class或genesym或eqtlTestsManager类的实例，这是一个奇怪的逻辑老功能的API的变化;使用旧的行为，呼吁GGtools ::: 。topFeats
参数：mgr
an instance of multffManager
一个multffManager实例
参数：mgrOrCTD
an instance of multffManager or a cisTransDirector instance
一个的multffManager实例或cisTransDirector的实例
参数：ffind
the index of the ff structure to use (typically chromosome number)
使用FF结构指数（通常染色体数目）
参数：start
left end of interval of interest
利率区间的左端
参数：end
right end of interval of interest
利率区间的右端
参数：snplocs
location structure for SNP (RangedData instance)
位置结构的SNP（RangedData实例）
参数：n
for topFeats, the number of features to report
topFeats，报告功能
参数：anno
name of a gene annotation package resolving the identifiers used in column names of ff matrix
基因注释包名解决在FF矩阵的列名使用的标识符
参数：useSym
logical indicating whether colnames of return should be gene symbols derived from anno
逻辑说明，是否回报colnames应是从anno的基因符号
参数：minMAF
numeric lower bound on minor allele frequency of SNPs to be considered
数字低势必要考虑的次要等位基因频率的SNP
参数：minGTF
numeric lower bound on minimum genotype frequency of SNPs to be considered
数字低约束的单核苷酸多态性被认为是最低的基因型频率
参数：...
see comment in USAGE and entries above
在用法和条目上面看到评论
Details
详情----------Details----------
X2chunk will obtain RAM resources for material on disk, so use with caution
，x2chunk将获得RAM磁盘上的物质资源，所以请谨慎使用
Note that gene symbols may map to multiple probes. The first hit is used by topFeats when used with sym=.
请注意，基因符号可能会映射到多个探针。 SYM =使用时先打由topFeats的。
作者（S）----------Author(s)----------
VJ Carey
举例----------Examples----------
## Not run: [＃无法运行：]
# build an smlSet with a small set of neighboring genes[建立与小的邻近基因组smlSet]
data(snpLocs20)
if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
library(illuminaHumanv1.db)
gOn20 = get("20", revmap(illuminaHumanv1CHR))
gLocs = geneRanges(gOn20, "illuminaHumanv1.db")
start = 10000000
end = 13500000
g2use_inds = which(ranges(gLocs)$chr20 %in% IRanges(start,end))
g2use_names = gLocs[g2use_inds,]$name
h20 = hmceuB36.2021[ probeId(g2use_names), ]
h20 = h20[chrnum(20),]
sn2use_inds = which(ranges(snpLocs20)$chr20 %in% IRanges(start,end))
od = getwd()
setwd(tempdir())
# create the ff manager instance[建立FF经理实例]
library(ff)
dd = eqtlTests(h20, ~male)
# extract the matrix[提取矩阵]
fc = X2chunk(dd, 1, start, end, snpLocs20, "illuminaHumanv1.db")
dim(fc)
fc[1:4,1:5]
setwd(od)
heatmap(fc[1:50,], Rowv=NA, Colv=NA, scale="none")
topFeats( rsid("rs6094162"), mgr=dd, 1, "illuminaHumanv1.db")
topFeats( genesym("MKKS"), mgr=dd, 1, "illuminaHumanv1.db")
## 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 19:51:33
