R常用統計 - 相關關係分析
阿新 • • 發佈:2020-07-26
資料格式
每行分別為表型和基因表達情況對應標量,每列分別為樣品名的矩陣。假定前9列為phenotype,從第10行起為gene_id,編寫簡單for迴圈如下:
script
require("lessR") library(lessR) data = read.table("c:/Users/****/Desktop/yourfile.txt", header = T,row.names = 1,na.strings = T,sep = "\t") #input your file results = NULL for (i in 1:9) {# for (j in 10:nrow(data)){ if (median(as.numeric(data[j,]))>=1e-5) { x = data[i,] y = data[j,] tem_res = Correlation(x, y, meth = "spearman", adjt = "fdr", heat_map = F) term_result = data.frame(row.names(data)[i],row.names(data)[j],tem_res$r,tem_res$pvalue) results = rbind(results,term_result) } } } colnames(results) = c("phenotype","gene_id","r_value","p_value") write.csv(results,"correlation_results.csv",row.names = F)