OmicShare Class 基迪奥生物信息在线课堂

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故事在城外

请问老师，这节课的代码在哪里可以下载到？

2349天前

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 2276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)]

2121天前

A1543274736

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")

}

2026天前

李有光

lambda数值应该在什么范围内啊

1775天前

biexiaomin98_163_com

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")

}

1624天前

hai178912522 回复 biexiaomin98\%163\%com ：

我的也是这个问题，你解决了吗？

#1 1571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 1540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 1540天前回复

kobee47 回复 hai178912522 ：

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

#4 1540天前回复

kobee47

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)

1540天前

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