{"id":61772,"date":"2024-11-19T15:18:06","date_gmt":"2024-11-19T07:18:06","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61772"},"modified":"2024-11-19T15:18:06","modified_gmt":"2024-11-19T07:18:06","slug":"%e7%a8%8b%e5%ba%8f%e8%bf%90%e8%a1%8c%e5%a4%aa%e4%b9%85%ef%bc%9f%e4%b8%8d%e5%a6%a8%e6%9d%a5%e8%af%95%e8%af%95%e5%a4%9a%e7%ba%bf%e7%a8%8b%e8%bf%90%e8%a1%8c%ef%bc%8cdopar%e8%ae%a9%e4%bd%a0%e7%9a%84","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61772","title":{"rendered":"\u7a0b\u5e8f\u8fd0\u884c\u592a\u4e45\uff1f\u4e0d\u59a8\u6765\u8bd5\u8bd5\u591a\u7ebf\u7a0b\u8fd0\u884c\uff0c%dopar%\u8ba9\u4f60\u7684\u7a0b\u5e8f\u5feb\u5230\u98de\u8d77"},"content":{"rendered":"\n

<\/h1>\n\n\n\n

\u5728\u505a\u6570\u636e\u5206\u6790\u65f6\uff0c\u6211\u4eec\u7ecf\u5e38\u9047\u5230\u9700\u8981for\u5faa\u73af\u7684\u7a0b\u5e8f\uff0c\u5982\u679cfor\u5faa\u73af\u5185\u7684\u64cd\u4f5c\u7b80\u5355\u8fd8\u597d\uff0c\u4f46\u662f\u6211\u4eec\u7ecf\u5e38\u9047\u5230\u5728for\u5faa\u73af\u5185\u505a\u590d\u6742\u64cd\u4f5c\u7684\u7a0b\u5e8f\uff0c\u8fd9\u79cd\u7a0b\u5e8f\u76f8\u5f53\u8017\u65f6\uff0c\u5fc5\u987b\u7b49\u524d\u4e00\u4e2a\u4efb\u52a1\u5b8c\u6210\u4e86\u624d\u8fdb\u884c\u4e0b\u4e00\u4e2a\u4efb\u52a1\uff0c\u5982\u679c\u6bcf\u4e2a\u4efb\u52a1\u90fd\u4e0e\u4e4b\u524d\u7684\u4efb\u52a1\u65e0\u5173\uff0c\u90a3\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528\u591a\u7ebf\u7a0b\u6765\u8fd0\u884c\u8fd9\u4e2afor\u5faa\u73af\u3002<\/p>\n\n\n\n

\u4e4b\u524d\u5c0f\u82b1\u5c31\u9047\u5230\u8fc7\u8ba1\u7b97mRNA\u4e0elncRNA\u76f8\u5173\u6027\u7684\u5206\u6790\uff0c\u5171\u6709116\u4e2amRNA\u548c4888\u4e2alncRNA\uff0c\u6837\u672c\u6570\u662f589\uff0c\u5982\u679c\u7528\u666e\u901a\u7684for\u5faa\u73af\u7684\u8bdd\u90a3\u5f97\u8fd0\u884c\u5230\u7334\u5e74\u9a6c\u6708\uff0c\u8fd8\u597d\u5c0f\u82b1\u6709\u670d\u52a1\u5668\uff0c\u53ef\u4ee5\u5728\u670d\u52a1\u5668\u4e0a\u591a\u7ebf\u7a0b\u8fd0\u884c\u3002\u8981\u662f\u60a8\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u53ef\u4ee5\u8054\u7cfb\u6211\uff0c\u5982\u679c\u60a8\u7684\u6570\u636e\u91cf\u6bd4\u8f83\u5927\u4e5f\u53ef\u4ee5\u8054\u7cfb\u5c0f\u82b1\u79df\u8d41\u9ad8\u6027\u4ef7\u6bd4\u7684\u670d\u52a1\u5668\u54e6\u3002<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\u6211\u4eec\u6765\u770b\u4e00\u4e0b\u6570\u636e\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u539f\u672c\u5c0f\u82b1\u4e5f\u662f\u7528\u666e\u901a\u7684for\u5faa\u73af\u8dd1\u7684\uff0c\u672c\u6765\u60f3\u7740\u60f3\u8ba9\u7a0b\u5e8f\u8fd0\u884c\u7740\uff0c\u6211\u53bb\u5403\u4e2a\u996d\u518d\u56de\u6765\u770b\uff0c\u7ed3\u679c\u5403\u5b8c\u996d\u53c8\u767b\u9646\u51e0\u4e2a\u5c0f\u65f6\u7a0b\u5e8f\u8fd8\u6ca1\u6709\u8fd0\u884c\u597d\uff1a<\/p>\n\n\n\n

up_glycolysis = read.table(“.\/input\/up_glycolysis.txt”, sep = “\\n”)$V1<\/p>\n\n\n\n

down_glycolysis = read.table(“.\/input\/down_glycolysis.txt”, sep = “\\n”)$V1<\/p>\n\n\n\n

diff_mRNA = c(up_glycolysis, down_glycolysis)<\/p>\n\n\n\n

diffLab = read.csv(“.\/input\/LUAD_lncRNA_diff.csv”)<\/p>\n\n\n\n

#diffLab = diffLab[-which(is.na(diffLab$X)),]<\/p>\n\n\n\n

diff_lncRNA = diffLab$X<\/p>\n\n\n\n

mRNA_data_norm = read.csv(“.\/input\/LUAD_mRNA_norm.csv”, row.names = 1)<\/p>\n\n\n\n

lncRNA_data_norm = read.csv(“.\/input\/LUAD_lncRNA_norm.csv”, row.names = 1)<\/p>\n\n\n\n

m_lnc_cor = matrix(0, nrow = length(diff_mRNA), ncol = length(diff_lncRNA))<\/p>\n\n\n\n

m_lnc_cor_p = matrix(0, nrow = length(diff_mRNA), ncol = length(diff_lncRNA))<\/p>\n\n\n\n

rownames(m_lnc_cor) = diff_mRNA<\/p>\n\n\n\n

colnames(m_lnc_cor) = diff_lncRNA<\/p>\n\n\n\n

rownames(m_lnc_cor_p) = diff_mRNA<\/p>\n\n\n\n

colnames(m_lnc_cor_p) = diff_lncRNA<\/p>\n\n\n\n

for(i in 1:length(diff_mRNA)){<\/p>\n\n\n\n

for(j in 1:length(diff_lncRNA)){<\/p>\n\n\n\n

m_lnc_cor[i, j] = cor(as.numeric(mRNA_data_norm[diff_mRNA[i],]), as.numeric(lncRNA_data_norm[diff_lncRNA[j],]))<\/p>\n\n\n\n

m_lnc_cor_p[i, j] = cor.test(as.numeric(mRNA_data_norm[diff_mRNA[i],]), as.numeric(lncRNA_data_norm[diff_lncRNA[j],]))[[3]]<\/p>\n\n\n\n

}<\/p>\n\n\n\n

}<\/p>\n\n\n\n

\u8fd9\u65f6\u5019\u6211\u60f3\u5230\uff0c\u65e2\u7136\u6211\u7684for\u5faa\u73af\u5185\u7684\u8bed\u53e5\u524d\u540e\u95f4\u7684\u8ba1\u7b97\u7ed3\u679c\u5e76\u4e0d\u4f1a\u6709\u5f71\u54cd\uff0c\u6240\u4ee5\u6211\u60f3\u5230\u4e86\u7528\u591a\u7ebf\u7a0b\u6765\u8fd0\u884c\uff1a<\/p>\n\n\n\n

## \u591a\u7ebf\u7a0b\u8fd0\u884c<\/p>\n\n\n\n

library(parallel)<\/p>\n\n\n\n

library(foreach)<\/p>\n\n\n\n

library(doParallel)<\/p>\n\n\n\n

# \u81ea\u5b9a\u4e49\u5408\u5e76\u51fd\u6570<\/p>\n\n\n\n

combine_results <- function(…) {<\/p>\n\n\n\n

# \u5c06…\u4e2d\u7684\u6240\u6709\u5217\u8868\u8f6c\u6362\u4e3a\u77e9\u9635\u7684\u5217<\/p>\n\n\n\n

lists <- list(…)<\/p>\n\n\n\n

result <- do.call(rbind, lapply(lists, function(lst) unlist(lst)))<\/p>\n\n\n\n

return(result)<\/p>\n\n\n\n

}<\/p>\n\n\n\n

# \u68c0\u6d4b\u53ef\u7528\u7684\u6838\u5fc3\u6570<\/p>\n\n\n\n

numCores <- detectCores()<\/p>\n\n\n\n

# \u521b\u5efa\u5e76\u6ce8\u518c\u96c6\u7fa4<\/p>\n\n\n\n

clus <- makeCluster(numCores)<\/p>\n\n\n\n

registerDoParallel(clus)<\/p>\n\n\n\n

start_time <- Sys.time()<\/p>\n\n\n\n

results <- foreach(i = 1:length(diff_mRNA), .combine=’combine_results’, .packages = c(“stats”)) %dopar% {<\/p>\n\n\n\n

temp_cor <- numeric(length(diff_lncRNA))<\/p>\n\n\n\n

temp_cor_p <- numeric(length(diff_lncRNA))<\/p>\n\n\n\n

for(j in 1:length(diff_lncRNA)) {<\/p>\n\n\n\n

temp_cor[j] <- cor(as.numeric(mRNA_data_norm[diff_mRNA[i],]), as.numeric(lncRNA_data_norm[diff_lncRNA[j],]))<\/p>\n\n\n\n

temp_cor_p[j] <- cor.test(as.numeric(mRNA_data_norm[diff_mRNA[i],]), as.numeric(lncRNA_data_norm[diff_lncRNA[j],]))$p.value<\/p>\n\n\n\n

}<\/p>\n\n\n\n

list(cor = temp_cor, p_value = temp_cor_p)<\/p>\n\n\n\n

}<\/p>\n\n\n\n

end_time <- Sys.time()<\/p>\n\n\n\n

# \u5173\u95ed\u96c6\u7fa4<\/p>\n\n\n\n

stopCluster(clus)<\/p>\n\n\n\n

time_taken_multi <- end_time – start_time<\/p>\n\n\n\n

print(time_taken_multi)<\/p>\n\n\n\n

m_lnc_cor = results[,1:length(diff_lncRNA)]<\/p>\n\n\n\n

m_lnc_cor_p = results[,(length(diff_lncRNA)+1):(2*length(diff_lncRNA))]<\/p>\n\n\n\n

rownames(m_lnc_cor) = diff_mRNA<\/p>\n\n\n\n

colnames(m_lnc_cor) = diff_lncRNA<\/p>\n\n\n\n

rownames(m_lnc_cor_p) = diff_mRNA<\/p>\n\n\n\n

colnames(m_lnc_cor_p) = diff_lncRNA<\/p>\n\n\n\n

saveRDS(m_lnc_cor, “.\/output\/m_lnc_cor.rds”)<\/p>\n\n\n\n

saveRDS(m_lnc_cor_p, “.\/output\/m_lnc_cor_p.rds”)<\/p>\n\n\n\n

\u8fd9\u662f\u7528htop\u547d\u4ee4\u67e5\u770b\u540e\u53f0\u8fd0\u884c\u72b6\u51b5\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u770b\u523056\u4e2a\u7ebf\u7a0b\u5168\u90e8\u5360\u6ee1\u4e86\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u6700\u540e\u53ea\u7528\u4e8611\u5206\u949f\u5c31\u7ed3\u675f\u4e86\u6218\u6597\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

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\u4ee3\u7801\u4e2d\u7684combine_results\u662f\u6211\u4eec\u81ea\u5b9a\u4e49\u7684\u5408\u5e76\u51fd\u6570\uff0c\u7528\u4e8e\u5c06\u591a\u7ebf\u7a0b\u8ba1\u7b97\u7684\u7ed3\u679c\u5408\u5e76\uff0c\u56e0\u4e3a\u6211\u4eec\u540c\u65f6\u8ba1\u7b97\u4e86\u76f8\u5173\u6027\u548c\u76f8\u5173\u6027pvalue\uff0c\u6240\u4ee5\u4e0d\u80fd\u7528\u666e\u901a\u7684rbind\u6216cbind\u5408\u5e76\u3002<\/p>\n\n\n\n

\u597d\u4e86\uff0c\u4eca\u5929\u7684\u77e5\u8bc6\u5c31\u5206\u4eab\u5230\u8fd9\u91cc\u4e86\uff0c\u5982\u679c\u5404\u4f4d\u89c9\u5f97\u81ea\u5df1\u8fd0\u884c\u4ee3\u7801\u592a\u9ebb\u70e6\uff0c\u6b22\u8fce\u7528\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177<\/strong>(<\/strong>http:\/\/www.biocloudservice.com\/home.html<\/strong>)<\/strong>\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u51fa\u60f3\u8981\u7684\u56fe\u5462<\/strong>\u3002<\/strong>\u4e00\u5bf8\u5149\u9634\u4e00\u5bf8\u91d1\uff0c\u5bf8\u91d1\u96be\u4e70\u5bf8\u5149\u9634\uff0c\u670d\u52a1\u5668\u53ef\u4ee5\u5927\u5927\u63d0\u5347\u6211\u4eec\u7684\u5de5\u4f5c\u6548\u7387\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u82b1\u79df\u8d41\u9ad8\u6027\u4ef7\u6bd4\u7684\u670d\u52a1\u5668\u54e6\u3002<\/strong><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

\u5728\u505a\u6570\u636e\u5206\u6790\u65f6\uff0c\u6211\u4eec\u7ecf\u5e38\u9047\u5230\u9700\u8981for\u5faa\u73af\u7684\u7a0b\u5e8f\uff0c\u5982\u679cfor\u5faa\u73af\u5185\u7684\u64cd\u4f5c\u7b80\u5355\u8fd8\u597d\uff0c\u4f46\u662f\u6211\u4eec\u7ecf\u5e38\u9047\u5230\u5728for\u5faa\u73af […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61772"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=61772"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61772\/revisions"}],"predecessor-version":[{"id":61776,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61772\/revisions\/61776"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61772"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61772"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61772"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}