AI代码解释 library(maftools)library(tidyverse)laml.gistic=readGistic(gisticAllLesionsFile="579436/all_lesions.conf_99.txt",gisticAmpGenesFile="579436/amp_genes.conf_99.txt",gisticDelGenesFile="579436/del_genes.conf_99.txt",gisticScoresFile="579436/scores.gistic",isTCGA=TRUE)##-Processing Gistic...
使用maftools画图 maftools这个包可以做一些拷贝数变异的可视化,比如上面展示的那种图,但是画出来也不好看,也没有什么自定义选项,很明显是达不到各位的审美水平的。 代码语言:javascript 代码运行次数:0 运行 AI代码解释 ## 使用maftools分析library(maftools)all.lesions<-"./TCGA_COAD_results/all_lesions.conf_90....
all.lesions <-"./TCGA_COAD_results/all_lesions.conf_90.txt" amp.genes <-"./TCGA_COAD_results/amp_genes.conf_90.txt" del.genes <-"./TCGA_COAD_results/del_genes.conf_90.txt" scores.gis <-"./TCGA_COAD_results/scores.gistic" coad.gistic = readGistic(gisticAllLesionsFile = all.lesion...
To configure viewer parameters create fileviewer.confwithin same directory in following format: This way you can set any parameter using python syntax. Any parameter specified here will overwrite parameters provided in command line. CNVpytor is not just command line tool but also Python package. ...
使用str函数查看一下注释文件Marer中包含的相关内容,结果显示:可以看到,其中包含了探针id,染色体的相关信息等内容。 fre<- Marker$freqcnv=="FALSE"table(fre) 根据提示的内容,判断freqcnv列中为FALSE的内容。 Marker<- Marker[fre,1:3]colnames(Marker) <- c("Marker_Name","Chromosome","Marker_Position")he...
## --Processing del_genes.conf_90.txt ## --Processing scores.gistic ## --Summarizing by samples gisticChromPlot(gistic = coad.gistic ,markBands ="all" ,ref.build ="hg38" ) # gisticBubblePlot(gistic = coad.gistic) 这个图和文献里看到的还是差距很大的!下面我们学习下用ggplot2画图!