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我一直在尝试在 R 中创建一个 qq 图。我很难使用我的结果，所以我尝试遵循“遗传病例对照研究中的基本统计分析，Clarke 等人”中的示例。

步骤 5, a, iii) 我已将路径和模型替换为必填字段，如下所示：

data<-read.table("C:\Users\X\Desktop\BIOM3006\Alternate/data.assoc.logistic",header=TRUE);pdf("C:\Users\X\Desktop\BIOM3006\Alternate/pvalue.qq.plot.pdf");

obs<-−log10(sort(data[data$TEST=="ADD",]$P));exp<-−log10(c(1:length(obs))/(length(obs)+ 1));plot(exp, 

obs<-ylab="Observed(−logP)",xlab="Expected(−logP)",ylim=c(0,20),xlim=c(0,7)) lines(c(0,7),c(0,7),col=1,lwd=2);dev.off()

这是我收到的错误消息：

data<-read.table("C:\Users\Tom\Desktop\BIOM3006\Alternate/data.assoc.logistic",header=TRUE);pdf("C:\Users\Tom\Desktop\BIOM3006\Alternate/pvalue.qq.plot.pdf");
Error: '\U' used without hex digits in character string starting ""C:\U"

obs<-−log10(sort(data[data$TEST=="ADD",]$P));exp<-−log10(c(1:length(obs))/(length(obs)+ 1));plot(exp, 
Error in log10(sort(data[data$TEST == "ADD", ]$P)) : 
 non-numeric argument to mathematical function

In addition: Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

obs<-ylab="Observed(−logP)",xlab="Expected(−logP)",ylim=c(0,20),xlim=c(0,7))
Error: unexpected ',' in "obs<-ylab="Observed(-logP)","

lines(c(0,7),c(0,7),col=1,lwd=2)
Error in plot.xy(xy.coords(x, y), type = type, ...) : 
plot.new has not been called yet

;dev.off()
Error: unexpected ';' in ";"

我仍然在掌握这个软件，所以如果我忽略了一些明显的东西，任何帮助都将不胜感激和抱歉。汤姆

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3 回答 3

0

我会说你非常接近，有一些格式问题需要一些小的修复（例如<-and之间没有空格-log），但除此之外它看起来还可以，尽管没有可重现的例子很难说。

data <- read.table("C:\Users\X\Desktop\BIOM3006\Alternate/data.assoc.logistic",header=TRUE)
pdf("C:\Users\X\Desktop\BIOM3006\Alternate/pvalue.qq.plot.pdf")
obs <- −log10(sort(data[data$TEST=="ADD",]$P))
exp<- −log10(c(1:length(obs))/(length(obs)+ 1))
plot(exp, obs, ylab="Observed(−logP)",xlab="Expected(−logP)",ylim=c(0,20),xlim=c(0,7)) lines(c(0,7),c(0,7),col=1,lwd=2))
dev.off()
于 2014-04-05T19:59:52.290 回答
0

对我来说它有效：我只是做了一些小的修改。查看数据<-read.table("data.assoc",header=TRUE); pdf("pvalue.qq.plot.pdf");

obs<--log10(sort(data[data$TEST=="ADD",]$P)); exp<--log10(c(1:length(obs))/(length(obs)+ 1));

plot(exp,ylab="Observed(−logP)",xlab="Expected(−logP)",ylim=c(0,20),xlim=c(0,7))

线(c(0,7),c(0,7),col=1,lwd=2);

dev.off()

于 2016-11-14T06:19:09.647 回答
0

我同意上述意见，问题不在于您的代码本身，而在于"\U".

顺便说一句，我发布了一个更简单的脚本，用于创建 QQ 图，并在您的示例中采用plink输出。

# If you call the script from bash it may include the name of your plink.qassoc file
args=(commandArgs(TRUE))
ARG = args[1]

# check libraries. It may download some from the Internet
if(!("methods" %in% rownames(installed.packages())))  
install.packages("methods")
library("methods")
if(!("ggplot2" %in% rownames(installed.packages())))  
install.packages("ggplot2")
library("ggplot2")

# Input data file (it is different for your file)
filename = paste ("../plink_files/", ARG, ".plink.qassoc.adjusted",sep="")
data = read.table (file = filename, header=T)

# Takes proability vector. 
PROB = data$UNADJ

# minus Log-P
logQQ = -log(data$QQ  ,10)
logP  = -log(PROB,10)

# QQ Plot
qqplot = ggplot (data = data, aes (x = logQQ, y = logP )) + geom_point(shape=1)
  qqplot = qqplot + xlab("Expected -logP values") + ylab("Observed -logP values")
  qqplot = qqplot + geom_abline (intercept = 0, slope = 1, color="red")
  qqplot = qqplot + ylim(0,max(logQQ,logP)) + xlim (0,max(logQQ,logP))

# Saving plot into a file
output = paste ("../results/", ARG, "_QQplot.jpg", sep="")
ggsave(output, plot = qqplot,width=6.47,height=4.67)
于 2016-04-19T13:57:57.127 回答