getMeans(Starr)
getMeans()所属R语言包：Starr
Get mean ChIP-signal over annotated features
获取平均注释功能的芯片信号
译者：生物统计家园网 机器人LoveR
描述----------Description----------
getMeans calculates the mean ChIP-signal over annotated features
getMeans注释功能，计算平均的芯片信号
用法----------Usage----------
getMeans(eSet, probeAnno, geneAnno, regions)
参数----------Arguments----------
参数：eSet
an ExpressionSet
1 ExpressionSet
参数：probeAnno
a probeAnno object for the given ExpressionSet
为给ExpressionSet probeAnno对象
参数：geneAnno
a data frame containing the annotation of the features of interest
一个数据框包含感兴趣的功能注释
参数： regions
a data frame, containing four columns. The pos columns is a character with values out of c("start", "region", "end"). upstream and downstream ar integers, indicating how many bases upstream and downstream from the specified position in the feature are included. level is an integer, that says at which level the rectangle in the lower device should be plotted. The numeration goes from the bottom to the ceiling. cor is the correlation of the region, which is plotted in the upper panel.
一个数据框，其中包含四列。在POS列是一个字符c值（“开始”，“区域”，“结束”）。上游和下游的的AR整数，表示多少碱基的上游和下游，在指定位置的功能包括。 level是一个整数，说在哪个级别的矩形应绘制在较低的设备。在记数从底部到天花板。心病是该区域的相关性，这是在上游面板绘制。
值----------Value----------
a list. Each entry contains the mean signals over the specified regions (in the regions data frame) of all features in geneAnno.
一个列表。每个条目包含的所有功能geneAnno在指定的区域（在该区域的数据框）的平均信号。
作者（S）----------Author(s)----------
Benedikt Zacher <a href="mailto:zacher@lmb.uni-muenchen.de">zacher@lmb.uni-muenchen.de</a>
参见----------See Also----------
getProfiles
getProfiles
举例----------Examples----------
## [＃]
# dataPath <- system.file("extdata", package="Starr")[< - 。系统数据通路（的“extdata”，包=“斯塔尔”）]
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))[bpmapChr1 < - readBpmap（file.path（数据通路，“Scerevisiae_tlg_chr1.bpmap”））]
# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), [CELS < - C（file.path（数据通路，“Rpb3_IP_chr1.cel”），file.path（数据通路，“wt_IP_chr1.cel”），]
# file.path(dataPath,"Rpb3_IP2_chr1.cel"))[file.path（数据通路，“Rpb3_IP2_chr1.cel”））]
# names <- c("rpb3_1", "wt_1","rpb3_2")[名< - （“rpb3_1”，“wt_1”，“rpb3_2”）]
# type <- c("IP", "CONTROL", "IP")[类型< - C（“知识产权”，“控制”，“知识产权”）]
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)[rpb3Chr1 < - readCelFile（bpmapChr1，CELS，名称，类型，featureData = TRUE，log.it = TRUE）]
# ips <- rpb3Chr1$type == "IP"[IPS <费用 - rpb3Chr1类型==“知识产权”]
# controls <- rpb3Chr1$type == "CONTROL"[控制<“ - rpb3Chr1 $ ==”控制“]
# rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")[rpb3_rankpercentile < - normalize.Probes（rpb3Chr1，方法=“rankpercentile”）]
# description <- c("Rpb3vsWT")[说明< - Ç（“Rpb3vsWT”）]
# rpb3_rankpercentile_ratio <- getRatio(rpb3_rankpercentile, ips, controls, description, fkt=median, featureData=FALSE)[rpb3_rankpercentile_ratio < - getRatio（rpb3_rankpercentile，IPS，控制，描述，FKT =中位数，featureData = FALSE）]
# probeAnnoChr1 <- bpmapToProbeAnno(bpmapChr1)[probeAnnoChr1 < - bpmapToProbeAnno（bpmapChr1的）]
# transcriptAnno <- read.gffAnno(file.path(dataPath, "transcriptAnno.gff"), feature="transcript")[transcriptAnno < - read.gffAnno（file.path功能=（数据通路，“transcriptAnno.gff”），“成绩单”）]
# filtered_orfs <- filterGenes(transcriptAnno, distance_us = 0, distance_ds = 0, minLength = 1000)[filtered_orfs < - filterGenes（transcriptAnno，distance_us = 0，= 0，minLength distance_ds = 1000）]
# pos <- c("start", "start", "start", "region", "region","region","region", "stop","stop","stop")[POS < - C（“开始”，“开始”，“开始”，“区域”，“区域”，“区域”，“区域”，“停止”，“停止”，“一站式”）]
# upstream <- c(500, 0, 250, 0, 0, 500, 500, 500, 0, 250)[上游< - C（500，0，250，0，0，500，500，500，0，250）]
# downstream <- c(0, 500, 250, 0, 500, 0, 500, 0, 500, 250)[下游< - C（0，500，250，0，500，0，500，0，500，250）]
# info <- data.frame(pos=pos, upstream=upstream, downstream=downstream, stringsAsFactors=FALSE)[信息< - 数据框（POS = POS，上游=上游，下游的下游，stringsAsFactors为FALSE）]
# means_rpb3 <- getMeans(rpb3_rankpercentile_ratio, probeAnnoChr1, transcriptAnno[which(transcriptAnno$name %in% filtered_orfs),], info)[means_rpb3 < - getMeans（rpb3_rankpercentile_ratio，probeAnnoChr1，transcriptAnno [（的transcriptAnno $名称％％filtered_orfs）]，INFO）]
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 2012-2-26 15:08:25
