请问老师,这节课的代码在哪里可以下载到?

924天前
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admin 回复 故事在城外

第一章的第一节,以及第二章的第一节资料下载那里。

#1 851天前 回复

将同一性状不同模型的曼哈顿图放在一起需要修改哪部分参数呢?

mlm <- read.table("lecture10_mlm_7.txt", header = T, comment.char = "", stringsAsFactors = F, check.names = F, fill = T)

traitID <- unique(mlm$Trait)

for(tr in traitID){

  outfile <- paste0(tr, "_mlm")

  sub <- subset(mlm, Trait == tr)[,c(2:4,7)]


696天前
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你好老师

为什么圈图最外层是黑的,没有标记密度而且标记密度也没有显示在曼哈顿图下面,你看一下代码哪里错了

setwd("D:/lecture10")

mlm <- read.table("lecture10_mlm_7.txt", header = T, comment.char = "", stringsAsFactors = F, check.names = F, fill = T)

traitID <- unique(mlm$Trait)

for(tr in traitID){

  outfile <- paste0(tr, "_mlm")

  sub <- subset(mlm, Trait == tr)[,c(2:4,7)]

  sub <- sub[-1,]

  threshold <- 0.01/nrow(sub[!is.na(sub$p),])

  print(threshold)

  CMplot(sub, threshold = threshold, amplify = F, memo = outfile,file="pdf")

}


601天前
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lambda数值应该在什么范围内啊


351天前
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谢工程师,您好!按照资料所给代码和数据,用CMplot画图,为什么圈图最外层是黑的,没有标记密度而且标记密度也没有显示在曼哈顿图下面。

setwd("D:/lecture10")

mlm <- read.table("lecture10_mlm_7.txt", header = T, comment.char = "", stringsAsFactors = F, check.names = F, fill = T)

traitID <- unique(mlm$Trait)

for(tr in traitID){

  outfile <- paste0(tr, "_mlm")

  sub <- subset(mlm, Trait == tr)[,c(2:4,7)]

  sub <- sub[-1,]

  threshold <- 0.01/nrow(sub[!is.na(sub$p),])

  print(threshold)

  CMplot(sub, threshold = threshold, amplify = F, memo = outfile,file="pdf")

}

199天前
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hai178912522 回复 biexiaomin98\%163\%com

我的也是这个问题,你解决了吗?

#1 147天前 回复

kobee47 回复 biexiaomin98\%163\%com

#Note: if the length of parameter \'chr.den.col\' is bigger than 1, SNP density that counts \n the number of SNP within given size(\'bin.size\') will be plotted.

#2 115天前 回复

kobee47 回复 biexiaomin98\%163\%com

library(CMplot)\nglm <- read.table(\"lecture10\%glm\%1.txt\", header = T, comment.char = \"\", stringsAsFactors = F, check.names = F)\ntraitID <- unique(glm$Trait)\nfor(tr in traitID){\n outfile <- paste0(tr, \"\%glm\")\n sub <- subset(glm, Trait == tr)[,c(2:4,6)]\n threshold <- 0.01/nrow(sub[!is.na(sub$p),])\n CMplot(sub, threshold = threshold, chr.den.col=c(\"darkgreen\", \"yellow\", \"red\"),amplify = F, memo = outfile)

#3 115天前 回复

kobee47 回复 hai178912522

加个代码 chr.den.col=c(\"darkgreen\", \"yellow\", \"red\")

#4 115天前 回复

library(CMplot)
glm <- read.table("lecture10_glm_1.txt", header = T, comment.char = "", stringsAsFactors = F, check.names = F)
traitID <- unique(glm$Trait)
for(tr in traitID){
  outfile <- paste0(tr, "_glm")
  sub <- subset(glm, Trait == tr)[,c(2:4,6)]
  threshold <- 0.01/nrow(sub[!is.na(sub$p),])
  CMplot(sub, threshold = threshold, chr.den.col=c("darkgreen", "yellow", "red"),amplify = F, memo = outfile)


115天前
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