plotFreqStat(aCGH)
plotFreqStat()所属R语言包：aCGH
frequency plots and significance analysis
频率的图和意义分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The main application of this function is to plot the frequency of changes.
此功能的主要应用是绘制频率的变化。
用法----------Usage----------
plotFreqStat(aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)),
chrominfo = human.chrom.info.Jul03,
X = TRUE, Y = FALSE,
rsp.uniq = unique(pheno),
all = length(rsp.uniq) == 1 && is.null(resT),
titles = if (all) "All Samples" else rsp.uniq,
cutplot = 0, thres = .25, factor = 2.5, ylm = c(-1, 1),
p.thres = c(.01, .05, .1), numaut = 22, onepage = TRUE,
colored = TRUE)
参数----------Arguments----------
参数：aCGH.obj
Object of class aCGH
对象类aCGH
参数：resT
Data frame having the same structure as the result of applying mt.maxT or mt.minP functions from Bioconductor's multtest package for multiple testing. The result is a data frame including the following 4 components: 'index', 'teststat', 'rawp' and 'adjp'.
数据框申请mt.maxT或mt.minPBioconductor的multtest多个测试包功能的结果具有相同的结构。其结果是一个数据框包括以下4个组成部分：“索引”，“teststat，rawp和adjp”。
参数：pheno
phenotype to compare.
表型的比较。
参数：chrominfo
Chromosomal information. Defaults to human.chrom.info.Jul03
染色体的信息。 human.chrom.info.Jul03默认
参数：X
Include X chromosome? Defaults to yes.
包括X染色体？默认为yes。
参数：Y
Include Y chromosome? Defaults to no.
包括Y染色体？默认没有。
参数：rsp.uniq
rsp.uniq specified the codes for the groups of interest. Default is the unique levels of the phenotype. Not used when all is T.
rsp.uniq指定为利益团体的代码。默认是独特的表型水平。时不使用all是T
参数：all
all specifies whether samples should be analyzed by subgroups (T) or together (F).
all指定样品是否应群（T）或（F）的分析。
参数：titles
titles names of the groups to be used. Default is the unique levels of the pheno.
titles要使用的组的名称。默认是pheno独特的水平。
参数：cutplot
only clones with at least cutplot frequency of gain and loss are plotted.
绘制至少cutplot损益的频率只克隆。
参数：thres
thres is either a vector providing unique threshold for each sample or a vector of the same length as number of samples (columns in data) providing sample-specific threshold. If aCGH.obj has non-null sd.samples, then thres is automatically replaced by factor times madGenome of aCGH object. Clone is considered to be gained if it is above the threshold and lost if it below negative threshold. Used for plotting the gain/loss frequency data as well as for clone screening and for significance analysis when threshold is TRUE.Defaults to 0.25
thres要么是矢量提供独特的阈值，每个样品或提供样品特定的阈值样本数（data列）相同长度的向量。如果aCGH.obj有非空sd.samples，然后thresfactoraCGH对象倍madGenome自动的更换。克隆被认为是上涨，如果它上面的阈值和丢失，如果它的阈值低于负。绘制频率增益/损耗数据，以及克隆筛选和意义分析时使用threshold0.25 TRUE.Defaults
参数：factor
factor specifies the number by which experimental variability should be multiplied. used only when sd.samples(aCGH.obj) is not NULL or when factor is greater than 0. Defaults to 2.5
factor指定的实验变异应乘以数量。只有当sd.samples（aCGH.obj）是不是NULL或因素是大于0时。默认2.5
参数：ylm
ylm vertical limits for the plot
ylm图垂直的限制
参数：p.thres
p.thres vector of p-value ciut-off to be plotted. computed conservatively as the threshold corresponding to a given adjusted p-value.
p.thres向量p值ciut要绘制。保守计算相应的一个给定的调整p值作为阈值。
参数：numaut
numaut number of the autosomes
numaut的染色体数
参数：onepage
onepage whether all plots are to be plotted on one page or different pages. When more than 2 groups are compared, we recommend multiple pages.
onepage所有图是否要绘制一个页面或不同页面上。当超过2组进行比较，我们建议多页。
参数：colored
Is plotting in color or not? Default is TRUE.
正在策划在颜色或不？默认值是TRUE。
举例----------Examples----------
data(colorectal)
## Use mt.maxT function from multtest package to test[＃使用mt.maxT的功能从multtest封装测试]
## differences in group means for each clone grouped by sex[按性别分组＃每个克隆组方式的差异]
colnames(phenotype(colorectal))
sex <- phenotype(colorectal)$sex
sex.na <- !is.na(sex)
colorectal.na <- colorectal[ ,sex.na, keep = TRUE ]
dat <- log2.ratios.imputed(colorectal.na)
resT.sex <- mt.maxT(dat, sex[sex.na], test = "t", B = 1000)
## Plot the result along the genome[＃绘制沿基因组的结果。]
plotFreqStat(colorectal.na, resT.sex, sex[sex.na],
titles = c("Male", "Female"))
## Adjust the p.values from previous exercise with "fdr"[＃调整从以前的演习与“FDR”的p.values]
## method and plot them[＃方法和图他们]
resT.sex.fdr <- resT.sex
resT.sex.fdr$adjp <- p.adjust(resT.sex.fdr$rawp, "fdr")
plotFreqStat(colorectal.na, resT.sex.fdr, sex[sex.na],
titles = c("Male", "Female"))
## Derive statistics and p-values for testing the linear association of[＃派生测试线性协会的统计数据和p值]
## age with the log2 ratios of each clone along the samples[＃每个克隆log2沿样品的比年龄]
age <- phenotype(colorectal)$age
age.na <- which(!is.na(age))
age <- age[age.na]
colorectal.na <- colorectal[, age.na]
stat.age <- aCGH.test(colorectal.na, age, test = "linear.regression", p.adjust.method = "fdr")
#separate into two groups: < 70 and > 70 and plot freqeuncies of gain and loss[分成两组：<70> 70，收益和损失的图freqeuncies]
#for each clone. Note that statistic plotted corresponds to linear coefficient[每个克隆。请注意，统计绘制对应的线性系数]
#for age variable[年龄变量]
plotFreqStat(colorectal.na, stat.age, ifelse(age < 70, 0, 1), titles =
c("Young", "Old"), X = FALSE, Y = FALSE)
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。
|
发表于 2012-2-25 11:00:45
