install.packages(\u201ctidyverse\u201d)<\/p>\n
BiocManager::install(“survcomp”)<\/p>\n
install.packages(“superpc”)<\/p>\n
install.packages(\u201csurvival\u201d)<\/p>\n
install.packages(“glmnet”)<\/p>\n
- \n
- \u8f7d\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n
library(superpc)<\/p>\n
library(survival)<\/p>\n
library(survcomp)<\/p>\n
library(tidyverse)<\/p>\n
library(glmnet)<\/p>\n
- \n
- \u8bfb\u53d6\u6570\u636e<\/li>\n<\/ol>\n
#TCGA.txt-\u8bad\u7ec3\u96c6\u6570\u636e\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e8c\u5217\u8868\u793a\u751f\u5b58\u72b6\u6001\uff0c\u7b2c\u4e09\u5217\u8868\u793a\u751f\u5b58\u65f6\u95f4\uff0c\u5176\u4ed6\u5217\u4e3a\u57fa\u56e0\u540d<\/p>\n
tcga <- read.table(“TCGA.txt”, header = T,sep = “\\t”, quote = “”, check.names = F)<\/p>\n
![\"Dingtalk_20230626145325\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/dingtalk_20230626145325.jpeg?resize=640%2C170\")
<\/p>\n#GSE57303-\u6d4b\u8bd5\u96c6\u6570\u636e\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u4fe1\u606f\uff0c\u7b2c\u4e8c\u5217\u8868\u793a\u751f\u5b58\u72b6\u6001\uff0c\u7b2c\u4e09\u5217\u8868\u793a\u751f\u5b58\u65f6\u95f4\uff0c\u5176\u4ed6\u5217\u4e3a\u57fa\u56e0\u540d.<\/p>\n
GSE57303 <- read.table(“GSE57303.txt”, header = T, sep = “\\t”, quote = “”, check.names = F)<\/p>\n
![\"Dingtalk_20230626150339\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/dingtalk_20230626150339.jpeg?resize=640%2C155\")
<\/p>\n- \n
- \u6240\u9700\u6570\u636e\u683c\u5f0f\u6574\u7406<\/li>\n<\/ol>\n
# \u751f\u6210\u5305\u542b2\u4e2a\u6570\u636e\u96c6\u7684\u5217\u8868<\/p>\n
mm <- list(TCGA = tcga,<\/p>\n
GSE57303 = GSE57303)<\/p>\n
# \u6570\u636e\u6807\u51c6\u5316<\/p>\n
mm <- lapply(mm,function(x){<\/p>\n
x[,-c(1:3)] <- scale(x[,-c(1:3)])<\/p>\n
return(x)})<\/p>\n
result <- data.frame()<\/p>\n
# TCGA\u4f5c\u4e3a\u8bad\u7ec3\u96c6<\/p>\n
est_data <- mm$TCGA<\/p>\n
#GSE57303\u4f5c\u4e3a\u6d4b\u8bd5\u96c6<\/p>\n
w<-mm$GSE57303<\/p>\n
#\u83b7\u5f97\u57fa\u56e0\u540d<\/p>\n
pre_var <- colnames(est_data)[-c(1:3)]<\/p>\n
#\u63d0\u53d6\u8bad\u7ec3\u96c6\u9700\u8981\u7684\u5217\u6570\u636e<\/p>\n
est_dd <- est_data[, c(‘OS.time’, ‘OS’, pre_var)]<\/p>\n
#\u63d0\u53d6\u6d4b\u8bd5\u96c6\u9700\u8981\u7684\u5217\u6570\u636e<\/p>\n
w <- w[, c(‘OS.time’, ‘OS’, pre_var)]<\/p>\n
5.superpc\u7b97\u6cd5\u8fdb\u884c\u6a21\u578b\u6784\u5efa<\/p>\n
#\u8bad\u7ec3\u96c6\u6570\u636e\u5217\u8868<\/p>\n
data <- list(x = t(est_dd[, -c(1,2)]), y = est_dd$OS.time, censoring.status = est_dd$OS, featurenames = colnames(est_dd)[-c(1, 2)])<\/p>\n
set.seed(123)<\/p>\n
#\u5229\u7528\u8bad\u7ec3\u96c6\u8fdb\u884c\u6a21\u578b\u6784\u5efa<\/p>\n
fit <- superpc.train(data = data,type = ‘survival’, s0.perc = 0.5) #default<\/p>\n
cv.fit <- superpc.cv(fit, data, n.threshold = 20, #default<\/p>\n
n.fold = 10,<\/p>\n
n.components = 3,<\/p>\n
min.features = 5,<\/p>\n
max.features = nrow(data$x),<\/p>\n
compute.fullcv = TRUE,<\/p>\n
compute.preval = TRUE)<\/p>\n
#\u6d4b\u8bd5\u96c6\u6570\u636e\u5217\u8868<\/p>\n
test <- list(x = t(w[,-c(1,2)]), y = w$OS.time, censoring.status = w$OS, featurenames = colnames(w)[-c(1,2)])<\/p>\n
#\u5229\u7528\u8bad\u7ec3\u96c6\u8fdb\u884c\u6a21\u578b\u9884\u6d4b<\/p>\n
ff <- superpc.predict(fit, data, test, threshold = cv.fit$thresholds[which.max(cv.fit[[“scor”]][1,])], n.components = 1)<\/p>\n
#\u5c06\u6570\u636e\u7c7b\u578b\u6539\u4e3a\u6570\u5b57<\/p>\n
rr <- as.numeric(ff$v.pred)<\/p>\n
rr2 <- cbind(w[,1:2], RS = rr)<\/p>\n
#\u8ba1\u7b97\u6a21\u578b\u7684\u9884\u6d4b\u6548\u80fd\u7684C\u6307\u6570<\/p>\n
cc<-data.frame(Cindex=as.numeric(summary(coxph(Surv(OS.time,OS)~ RS,rr2))$concordance[1])) %>%<\/p>\n
rownames_to_column(‘ID’)<\/p>\n
cc$Model <- paste0(‘SuperPC’)<\/p>\n
result <- rbind(result, cc)<\/p>\n
6.Ridge\u7b97\u6cd5\u8fdb\u884c\u6a21\u578b\u6784\u5efa<\/p>\n
#\u6a21\u578b\u6784\u5efa<\/p>\n
x1 <- as.matrix(est_dd[, pre_var])<\/p>\n
x2 <- as.matrix(Surv(est_dd$OS.time, est_dd$OS))<\/p>\n
set.seed(seed)<\/p>\n
fit = glmnet(x1, x2, family = “binomial”, alpha = 0, lambda = NULL)<\/p>\n
cvfit = cv.glmnet(x1, x2,<\/p>\n
nfold = 10, #\u4f8b\u6587\u63cf\u8ff0\uff1a10-fold cross-validation<\/p>\n
family = “binomial”,<\/p>\n
type.measure = “class”<\/p>\n
)<\/p>\n
#\u6a21\u578b\u9884\u6d4b<\/p>\n
rs = as.numeric(predict(fit, type = ‘response’, newx = as.matrix(w[, -c(1,2)]), s = cvfit$lambda.min))<\/p>\n
rr2 <- cbind(w[,1:2], RS = rs)<\/p>\n
##\u8ba1\u7b97\u6a21\u578b\u7684\u9884\u6d4b\u6548\u80fd\u7684C\u6307\u6570<\/p>\n
cc <- data.frame(Cindex = as.numeric(summary(coxph(Surv(OS.time,OS) ~ RS, rr2))$concordance[1])) %>%<\/p>\n
rownames_to_column(‘ID’)<\/p>\n
cc$Model <- paste0(‘Ridge’)<\/p>\n
Result <- rbind(result, cc)<\/p>\n
write.table(Result,file=”superpc_ridge.txt”,row.names=F,col.names=T,sep=”\\t”,quote=F)<\/p>\n
![\"Dingtalk_20230626163309\"](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/dingtalk_20230626163309.jpeg?resize=640%2C45\")
<\/p>\n\u5c0f\u679c\u6700\u7ec8\u987a\u5229\u7684\u5229\u7528supersc\u548cRidge\u4e24\u79cd\u7b97\u6cd5\u8fdb\u884c\u4e86\u6a21\u578b\u6784\u5efa\u548c\u9884\u6d4b\uff0c\u5e76\u8ba1\u7b97\u4e86\u9884\u6d4b\u6548\u80fdC\u6307\u6570\uff0c\u6765\u5224\u65ad\u6a21\u578b\u7684\u597d\u574f\uff0c\u673a\u5668\u5b66\u4e60\u76f8\u5173\u7684\u5176\u4ed6\u5206\u6790\u5185\u5bb9\u6b22\u8fce\u5c1d\u8bd5\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u4e91\u5e73\u53f0\u751f\u7269\u4fe1\u606f\u5206\u6790\u5c0f\u5de5\u5177\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html\uff0c\u4e3b\u8981\u5305\u62eclasso\u56de\u5f52\u6a21\u578b\u7b5b\u9009\u7279\u5f81\u57fa\u56e0(http:\/\/www.biocloudservice.com\/116\/116.php),\u968f\u673a\u68ee\u6797\u7684\u5341\u6298\u4ea4\u53c9\u9a8c\u8bc1(http:\/\/www.biocloudservice.com\/646\/646.php),svm-ref\u652f\u6301\u5411\u91cf\u673a\u7684\u673a\u5668\u5b66\u4e60(http:\/\/www.biocloudservice.com\/372\/372.php)\u7b49\u673a\u5668\u5b66\u4e60\u76f8\u5173\u7684\u5c0f\u5de5\u5177\uff0c\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6b22\u8fce\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u5b66\u4e60\uff0c\u4e0b\u671f\u518d\u89c1\u5965\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
\u673a\u5668\u5b66\u4e60\uff0c\u5728\u751f\u4fe1\u6587\u7ae0\u4e2d\u51fa\u73b0\u7684\u9891\u7387\u8d8a\u6765\u8d8a\u9ad8\uff0c\u6210\u4e3a\u4e0d\u53ef\u6216\u7f3a\u7684\u4e00\u90e8\u5206\u5206\u6790\u5185\u5bb9\uff0c\u4eca\u5929\u5c0f\u679c\u60f3\u5e26\u7740\u5927\u5bb6\u5b66\u4e60\u4e00\u4e0b\u751f\u5b58\u76f8\u5173\u673a\u5668 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","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\/24297"}],"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=24297"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24297\/revisions"}],"predecessor-version":[{"id":24301,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24297\/revisions\/24301"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24297"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24297"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24297"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
- \u6240\u9700\u6570\u636e\u683c\u5f0f\u6574\u7406<\/li>\n<\/ol>\n
- \u8bfb\u53d6\u6570\u636e<\/li>\n<\/ol>\n