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歡迎來(lái)到醫(yī)科研，這里是白介素2的讀書(shū)筆記，跟我一起聊臨床與科研的故事, 生物醫(yī)學(xué)數(shù)據(jù)挖掘，R語(yǔ)言，TCGA、GEO, SEER數(shù)據(jù)挖掘。
KM生存分析 如何取最佳cutoff1library(survival)
2library(survminer)
3## Loading required package: ggplot2
4## Loading required package: ggpubr
5## Loading required package: magrittr
surv_cutpoint函數(shù)data：包含生存數(shù)據(jù)和連續(xù)變量的的數(shù)據(jù)框 time, event：column names containing time and event data, respectively. Event values sould be 0 or 1.
官方示例 1# 0. Load some data
2data(myeloma)
3head(myeloma)
4## molecular_group chr1q21_status treatment event time CCND1
5## GSM50986 Cyclin D-1 3 copies TT2 0 69.24 9908.4
6## GSM50988 Cyclin D-2 2 copies TT2 0 66.43 16698.8
7## GSM50989 MMSET 2 copies TT2 0 66.50 294.5
8## GSM50990 MMSET 3 copies TT2 1 42.67 241.9
9## GSM50991 MAF <NA> TT2 0 65.00 472.6
10## GSM50992 Hyperdiploid 2 copies TT2 0 65.20 664.1
11## CRIM1 DEPDC1 IRF4 TP53 WHSC1
12## GSM50986 420.9 523.5 16156.5 10.0 261.9
13## GSM50988 52.0 21.1 16946.2 1056.9 363.8
14## GSM50989 617.9 192.9 8903.9 1762.8 10042.9
15## GSM50990 11.9 184.7 11894.7 946.8 4931.0
16## GSM50991 38.8 212.0 7563.1 361.4 165.0
17## GSM50992 16.9 341.6 16023.4 2096.3 569.2
1. Determine the optimal cutpoint of variables1res.cut <- surv_cutpoint(myeloma, time = "time", event = "event",
2 variables = c("DEPDC1", "WHSC1", "CRIM1"))
3
4summary(res.cut)
5## cutpoint statistic
6## DEPDC1 279.8 4.275452
7## WHSC1 3205.6 3.361330
8## CRIM1 82.3 1.968317
2. Plot cutpoint for DEPDC11# palette = "npg" (nature publishing group), see ?ggpubr::ggpar
2plot(res.cut, "DEPDC1", palette = "npg")
3## $DEPDC1
 image.png3. Categorize variables1res.cat <- surv_categorize(res.cut)
2head(res.cat)
3## time event DEPDC1 WHSC1 CRIM1
4## GSM50986 69.24 0 high low high
5## GSM50988 66.43 0 low low low
6## GSM50989 66.50 0 low high high
7## GSM50990 42.67 1 low high low
8## GSM50991 65.00 0 low low low
9## GSM50992 65.20 0 high low low
4. Fit survival curves and visualize1library("survival")
2fit <- survfit(Surv(time, event) ~DEPDC1, data = res.cat)
3ggsurvplot(fit, data = res.cat, risk.table = TRUE, conf.int = TRUE)
 image.png參考資料官方文檔
本期內(nèi)容就到這里，我是白介素2，下期再見(jiàn)，點(diǎn)擊下方框框留言。
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